Starting phenix.real_space_refine on Wed Feb 4 15:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9li5_63111/02_2026/9li5_63111.map" } resolution = 3.9 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= 0.006 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7263 2.51 5 N 1899 2.21 5 O 2021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 11237 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11237 Classifications: {'peptide': 1422} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1363} Chain breaks: 2 Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 11237 At special positions: 0 Unit cell: (117.7, 118.8, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2021 8.00 N 1899 7.00 C 7263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 524.1 milliseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 60.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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 34 Processing helix chain 'A' and resid 38 through 59 removed outlier: 3.623A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.988A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 4.003A pdb=" N LEU A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 removed outlier: 4.171A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 147 through 162 removed outlier: 4.753A pdb=" N GLY A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.269A pdb=" N TYR A 168 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 192 removed outlier: 3.503A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.845A pdb=" N ILE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.722A pdb=" N THR A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.511A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.664A pdb=" N HIS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.037A pdb=" N ALA A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 removed outlier: 3.685A pdb=" N TRP A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 4.521A pdb=" N ASN A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.019A pdb=" N ILE A 341 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 342 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 4.128A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.621A pdb=" N ARG A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.585A pdb=" N ARG A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Proline residue: A 424 - end of helix removed outlier: 3.701A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.887A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.986A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.603A pdb=" N GLY A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.513A pdb=" N VAL A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 513 removed outlier: 3.634A pdb=" N SER A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 removed outlier: 3.709A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.580A pdb=" N PHE A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'A' and resid 567 through 572 removed outlier: 3.980A pdb=" N PHE A 571 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET A 572 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 594 removed outlier: 3.757A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 582 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 removed outlier: 3.576A pdb=" N LEU A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.597A pdb=" N ALA A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 741 through 757 removed outlier: 3.626A pdb=" N ASN A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 removed outlier: 3.564A pdb=" N GLY A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 778 " --> pdb=" O VAL A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.832A pdb=" N GLY A 788 " --> pdb=" O ARG A 785 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 789' Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.521A pdb=" N PHE A 801 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 803 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 804 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 805 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.593A pdb=" N SER A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 839 Processing helix chain 'A' and resid 904 through 916 removed outlier: 3.866A pdb=" N LEU A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 909 " --> pdb=" O TRP A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 941 removed outlier: 3.657A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 923 " --> pdb=" O TRP A 919 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS A 927 " --> pdb=" O MET A 923 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR A 931 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.628A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 3.790A pdb=" N LEU A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 992 removed outlier: 4.489A pdb=" N TYR A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 996 removed outlier: 3.519A pdb=" N MET A 996 " --> pdb=" O HIS A 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 993 through 996' Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.686A pdb=" N LYS A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 4.316A pdb=" N ASN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A1048 " --> pdb=" O GLN A1044 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 3.780A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1066 Processing helix chain 'A' and resid 1067 through 1072 Processing helix chain 'A' and resid 1085 through 1090 removed outlier: 3.615A pdb=" N SER A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1085 through 1090' Processing helix chain 'A' and resid 1092 through 1097 removed outlier: 3.867A pdb=" N TYR A1096 " --> pdb=" O ARG A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1104 Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 3.656A pdb=" N ALA A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1114 No H-bonds generated for 'chain 'A' and resid 1112 through 1114' Processing helix chain 'A' and resid 1118 through 1139 removed outlier: 3.673A pdb=" N ASN A1122 " --> pdb=" O MET A1118 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE A1132 " --> pdb=" O ASN A1128 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A1136 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1147 removed outlier: 3.639A pdb=" N LEU A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A1146 " --> pdb=" O TRP A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1165 removed outlier: 3.807A pdb=" N ALA A1162 " --> pdb=" O THR A1158 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1182 Processing helix chain 'A' and resid 1188 through 1200 removed outlier: 4.087A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 3.506A pdb=" N GLU A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1217 removed outlier: 4.523A pdb=" N TYR A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1212 through 1217' Processing helix chain 'A' and resid 1281 through 1290 removed outlier: 3.974A pdb=" N LEU A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1317 through 1319 No H-bonds generated for 'chain 'A' and resid 1317 through 1319' Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.580A pdb=" N LEU A1348 " --> pdb=" O ASN A1344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1352 " --> pdb=" O LEU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1362 Processing helix chain 'A' and resid 1373 through 1377 removed outlier: 3.693A pdb=" N GLY A1376 " --> pdb=" O SER A1373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A1377 " --> pdb=" O GLU A1374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1373 through 1377' Processing helix chain 'A' and resid 1380 through 1396 removed outlier: 3.927A pdb=" N ARG A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A1396 " --> pdb=" O ALA A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1425 removed outlier: 3.853A pdb=" N ALA A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A1425 " --> pdb=" O ILE A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1443 removed outlier: 3.595A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A1442 " --> pdb=" O THR A1439 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A1443 " --> pdb=" O ILE A1440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1438 through 1443' Processing helix chain 'A' and resid 1459 through 1466 removed outlier: 3.693A pdb=" N ASN A1466 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1477 removed outlier: 3.517A pdb=" N VAL A1475 " --> pdb=" O PHE A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1500 removed outlier: 3.729A pdb=" N ALA A1483 " --> pdb=" O GLY A1479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A1487 " --> pdb=" O ALA A1483 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A1496 " --> pdb=" O ASP A1492 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1497 " --> pdb=" O ASN A1493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 635 through 639 removed outlier: 5.555A pdb=" N ILE A 635 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 614 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 615 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 760 through 763 removed outlier: 6.216A pdb=" N VAL A 645 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 807 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 4.880A pdb=" N ASP A1246 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG A1299 " --> pdb=" O ASP A1246 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1297 " --> pdb=" O VAL A1248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1399 through 1403 removed outlier: 6.141A pdb=" N LEU A1400 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A1433 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A1402 " --> pdb=" O ILE A1433 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL A1272 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS A1271 " --> pdb=" O LYS A1445 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU A1447 " --> pdb=" O LYS A1271 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A1273 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A1449 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A1275 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1448 " --> pdb=" O GLN A1455 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1331 through 1332 379 hydrogen bonds defined for protein. 1089 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: 2.02 Time building geometry restraints manager: 1.19 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: 2887 1.33 - 1.45: 2298 1.45 - 1.57: 6206 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 11485 Sorted by residual: bond pdb=" CB ILE A1130 " pdb=" CG2 ILE A1130 " ideal model delta sigma weight residual 1.521 1.414 0.107 3.30e-02 9.18e+02 1.05e+01 bond pdb=" CB MET A1137 " pdb=" CG MET A1137 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.92e+00 bond pdb=" CG GLN A 359 " pdb=" CD GLN A 359 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.74e+00 bond pdb=" CB TRP A 260 " pdb=" CG TRP A 260 " ideal model delta sigma weight residual 1.498 1.414 0.084 3.10e-02 1.04e+03 7.27e+00 bond pdb=" CB ASN A 363 " pdb=" CG ASN A 363 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.75e+00 ... (remaining 11480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14834 2.53 - 5.05: 636 5.05 - 7.58: 103 7.58 - 10.11: 17 10.11 - 12.64: 1 Bond angle restraints: 15591 Sorted by residual: angle pdb=" CA TRP A 265 " pdb=" CB TRP A 265 " pdb=" CG TRP A 265 " ideal model delta sigma weight residual 113.60 123.40 -9.80 1.90e+00 2.77e-01 2.66e+01 angle pdb=" C TYR A 369 " pdb=" N ARG A 370 " pdb=" CA ARG A 370 " ideal model delta sigma weight residual 122.38 114.54 7.84 1.81e+00 3.05e-01 1.87e+01 angle pdb=" C GLU A 4 " pdb=" N PHE A 5 " pdb=" CA PHE A 5 " ideal model delta sigma weight residual 120.72 127.69 -6.97 1.67e+00 3.59e-01 1.74e+01 angle pdb=" CA TRP A 945 " pdb=" CB TRP A 945 " pdb=" CG TRP A 945 " ideal model delta sigma weight residual 113.60 121.44 -7.84 1.90e+00 2.77e-01 1.70e+01 angle pdb=" CA ALA A 23 " pdb=" C ALA A 23 " pdb=" N ASN A 24 " ideal model delta sigma weight residual 116.84 123.89 -7.05 1.71e+00 3.42e-01 1.70e+01 ... (remaining 15586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 6344 14.70 - 29.41: 421 29.41 - 44.11: 67 44.11 - 58.81: 5 58.81 - 73.52: 1 Dihedral angle restraints: 6838 sinusoidal: 2726 harmonic: 4112 Sorted by residual: dihedral pdb=" CA THR A 974 " pdb=" C THR A 974 " pdb=" N LEU A 975 " pdb=" CA LEU A 975 " ideal model delta harmonic sigma weight residual 180.00 145.07 34.93 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA THR A 552 " pdb=" C THR A 552 " pdb=" N PRO A 553 " pdb=" CA PRO A 553 " ideal model delta harmonic sigma weight residual -180.00 -146.45 -33.55 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA LEU A1066 " pdb=" C LEU A1066 " pdb=" N LEU A1067 " pdb=" CA LEU A1067 " ideal model delta harmonic sigma weight residual 180.00 149.43 30.57 0 5.00e+00 4.00e-02 3.74e+01 ... (remaining 6835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 894 0.043 - 0.086: 544 0.086 - 0.129: 266 0.129 - 0.172: 72 0.172 - 0.215: 11 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU A1045 " pdb=" CB LEU A1045 " pdb=" CD1 LEU A1045 " pdb=" CD2 LEU A1045 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA TYR A 369 " pdb=" N TYR A 369 " pdb=" C TYR A 369 " pdb=" CB TYR A 369 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1784 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 423 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 424 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 243 " -0.059 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A 244 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 945 " 0.021 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP A 945 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 945 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 945 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 945 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 945 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 945 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 945 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 945 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 945 " -0.001 2.00e-02 2.50e+03 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3417 2.81 - 3.33: 9737 3.33 - 3.85: 17211 3.85 - 4.38: 19655 4.38 - 4.90: 33028 Nonbonded interactions: 83048 Sorted by model distance: nonbonded pdb=" O PRO A 703 " pdb=" OH TYR A 755 " model vdw 2.283 3.040 nonbonded pdb=" O ALA A 753 " pdb=" OG SER A 756 " model vdw 2.300 3.040 nonbonded pdb=" O SER A 943 " pdb=" OG SER A 943 " model vdw 2.303 3.040 nonbonded pdb=" O LEU A1348 " pdb=" OG SER A1351 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" OE2 GLU A 511 " model vdw 2.326 3.040 ... (remaining 83043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.013 0.107 11486 Z= 0.582 Angle : 1.191 12.637 15593 Z= 0.628 Chirality : 0.065 0.215 1787 Planarity : 0.008 0.100 1968 Dihedral : 10.007 73.518 4187 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.15 % 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: -5.42 (0.16), residues: 1416 helix: -4.24 (0.09), residues: 831 sheet: -0.88 (0.65), residues: 72 loop : -2.44 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 910 TYR 0.029 0.004 TYR A 959 PHE 0.047 0.004 PHE A 361 TRP 0.054 0.005 TRP A 945 HIS 0.016 0.003 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.01340 (11485) covalent geometry : angle 1.19073 (15591) SS BOND : bond 0.00594 ( 1) SS BOND : angle 0.95872 ( 2) hydrogen bonds : bond 0.33774 ( 379) hydrogen bonds : angle 10.75226 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.9198 (t80) cc_final: 0.8894 (t80) REVERT: A 145 PHE cc_start: 0.8043 (m-80) cc_final: 0.7401 (t80) REVERT: A 278 SER cc_start: 0.9387 (m) cc_final: 0.9053 (t) REVERT: A 535 LEU cc_start: 0.8988 (mt) cc_final: 0.8420 (tt) REVERT: A 708 LYS cc_start: 0.8999 (tttt) cc_final: 0.8786 (ttmm) REVERT: A 919 TRP cc_start: 0.7821 (t60) cc_final: 0.7486 (t60) REVERT: A 930 LEU cc_start: 0.9278 (tp) cc_final: 0.8615 (tt) REVERT: A 1274 ILE cc_start: 0.9183 (mt) cc_final: 0.8771 (mt) REVERT: A 1322 ILE cc_start: 0.8988 (mt) cc_final: 0.8626 (mp) REVERT: A 1393 LEU cc_start: 0.9373 (mt) cc_final: 0.9104 (mt) REVERT: A 1462 ASN cc_start: 0.9327 (m-40) cc_final: 0.8964 (p0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1284 time to fit residues: 45.4078 Evaluate side-chains 159 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 295 ASN A 720 HIS A 800 HIS A 998 HIS A1078 GLN A1128 ASN ** A1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102691 restraints weight = 19929.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100437 restraints weight = 20122.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100782 restraints weight = 16371.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101582 restraints weight = 12645.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102214 restraints weight = 10725.903| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11486 Z= 0.138 Angle : 0.677 8.431 15593 Z= 0.353 Chirality : 0.043 0.146 1787 Planarity : 0.005 0.073 1968 Dihedral : 6.423 23.619 1544 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.20 % Allowed : 7.17 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.88 (0.19), residues: 1416 helix: -2.99 (0.13), residues: 844 sheet: -0.56 (0.66), residues: 68 loop : -1.71 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 906 TYR 0.024 0.002 TYR A 369 PHE 0.027 0.001 PHE A 394 TRP 0.026 0.002 TRP A 945 HIS 0.002 0.001 HIS A1267 Details of bonding type rmsd covalent geometry : bond 0.00297 (11485) covalent geometry : angle 0.67666 (15591) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.37474 ( 2) hydrogen bonds : bond 0.05561 ( 379) hydrogen bonds : angle 5.89273 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.7918 (t80) cc_final: 0.7449 (t80) REVERT: A 145 PHE cc_start: 0.7959 (m-80) cc_final: 0.7196 (t80) REVERT: A 149 TYR cc_start: 0.8951 (t80) cc_final: 0.8585 (t80) REVERT: A 168 TYR cc_start: 0.8781 (m-80) cc_final: 0.8567 (m-80) REVERT: A 228 GLU cc_start: 0.7460 (tt0) cc_final: 0.7002 (pt0) REVERT: A 282 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6361 (tp30) REVERT: A 403 MET cc_start: 0.6744 (tmm) cc_final: 0.6403 (tmm) REVERT: A 666 LEU cc_start: 0.8681 (mt) cc_final: 0.7889 (mt) REVERT: A 919 TRP cc_start: 0.7530 (t60) cc_final: 0.7132 (t60) REVERT: A 923 MET cc_start: 0.7854 (tpp) cc_final: 0.7602 (tpp) REVERT: A 930 LEU cc_start: 0.9113 (tp) cc_final: 0.8473 (tt) REVERT: A 977 ASN cc_start: 0.9035 (t0) cc_final: 0.8573 (t0) REVERT: A 1013 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7904 (tt) REVERT: A 1039 MET cc_start: 0.8632 (mmt) cc_final: 0.8394 (mmt) REVERT: A 1179 MET cc_start: 0.8792 (tpp) cc_final: 0.8327 (mmm) REVERT: A 1402 LEU cc_start: 0.9146 (mt) cc_final: 0.8864 (tt) REVERT: A 1462 ASN cc_start: 0.9308 (m-40) cc_final: 0.8879 (p0) outliers start: 27 outliers final: 13 residues processed: 205 average time/residue: 0.1133 time to fit residues: 32.9245 Evaluate side-chains 159 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 138 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 81 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 331 GLN A 395 GLN A 739 ASN A 954 HIS ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 ASN A1493 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098160 restraints weight = 20336.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093473 restraints weight = 16860.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094473 restraints weight = 15826.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094866 restraints weight = 12224.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094960 restraints weight = 11559.437| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11486 Z= 0.249 Angle : 0.736 10.207 15593 Z= 0.370 Chirality : 0.047 0.154 1787 Planarity : 0.005 0.070 1968 Dihedral : 6.089 24.708 1544 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.69 % Allowed : 9.78 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.11 (0.21), residues: 1416 helix: -2.23 (0.15), residues: 859 sheet: -0.21 (0.71), residues: 67 loop : -1.63 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1354 TYR 0.026 0.002 TYR A 369 PHE 0.019 0.002 PHE A 394 TRP 0.023 0.002 TRP A 945 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00571 (11485) covalent geometry : angle 0.73605 (15591) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.53612 ( 2) hydrogen bonds : bond 0.05219 ( 379) hydrogen bonds : angle 5.48004 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.7404 (t) cc_final: 0.7152 (m) REVERT: A 73 TYR cc_start: 0.7809 (t80) cc_final: 0.7193 (t80) REVERT: A 145 PHE cc_start: 0.7905 (m-80) cc_final: 0.7584 (t80) REVERT: A 149 TYR cc_start: 0.9009 (t80) cc_final: 0.8611 (t80) REVERT: A 228 GLU cc_start: 0.7517 (tt0) cc_final: 0.6716 (pt0) REVERT: A 282 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: A 291 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 323 LEU cc_start: 0.9059 (tp) cc_final: 0.8819 (tt) REVERT: A 535 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 568 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: A 571 PHE cc_start: 0.6277 (t80) cc_final: 0.5648 (t80) REVERT: A 666 LEU cc_start: 0.8743 (mt) cc_final: 0.7991 (mt) REVERT: A 919 TRP cc_start: 0.7724 (t60) cc_final: 0.7418 (t60) REVERT: A 923 MET cc_start: 0.7776 (tpp) cc_final: 0.7373 (tpt) REVERT: A 930 LEU cc_start: 0.9195 (tp) cc_final: 0.8536 (tt) REVERT: A 1013 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8054 (tt) REVERT: A 1039 MET cc_start: 0.8677 (mmt) cc_final: 0.8392 (mmt) REVERT: A 1179 MET cc_start: 0.8909 (tpp) cc_final: 0.8456 (mmm) REVERT: A 1402 LEU cc_start: 0.9173 (mt) cc_final: 0.8907 (tt) REVERT: A 1462 ASN cc_start: 0.9347 (m-40) cc_final: 0.8945 (p0) outliers start: 33 outliers final: 16 residues processed: 170 average time/residue: 0.1000 time to fit residues: 24.9234 Evaluate side-chains 158 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 415 GLN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101232 restraints weight = 20103.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098020 restraints weight = 18414.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098967 restraints weight = 16572.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099530 restraints weight = 12419.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099844 restraints weight = 11036.436| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11486 Z= 0.129 Angle : 0.621 12.886 15593 Z= 0.307 Chirality : 0.042 0.142 1787 Planarity : 0.004 0.058 1968 Dihedral : 5.439 20.920 1544 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.12 % Allowed : 11.82 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -2.56 (0.21), residues: 1416 helix: -1.78 (0.16), residues: 870 sheet: -0.09 (0.70), residues: 68 loop : -1.38 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.019 0.001 TYR A 369 PHE 0.011 0.001 PHE A 109 TRP 0.018 0.001 TRP A 265 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00293 (11485) covalent geometry : angle 0.62145 (15591) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.40833 ( 2) hydrogen bonds : bond 0.04046 ( 379) hydrogen bonds : angle 4.82253 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.7268 (t) cc_final: 0.6955 (m) REVERT: A 73 TYR cc_start: 0.7801 (t80) cc_final: 0.7353 (t80) REVERT: A 145 PHE cc_start: 0.7821 (m-80) cc_final: 0.7589 (t80) REVERT: A 149 TYR cc_start: 0.8856 (t80) cc_final: 0.8532 (t80) REVERT: A 228 GLU cc_start: 0.7498 (tt0) cc_final: 0.6791 (pt0) REVERT: A 282 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6492 (tp30) REVERT: A 403 MET cc_start: 0.6920 (tmm) cc_final: 0.6619 (tmm) REVERT: A 666 LEU cc_start: 0.8730 (mt) cc_final: 0.8055 (mt) REVERT: A 702 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 919 TRP cc_start: 0.7583 (t60) cc_final: 0.7232 (t60) REVERT: A 923 MET cc_start: 0.7784 (tpp) cc_final: 0.7419 (tpt) REVERT: A 999 SER cc_start: 0.9213 (m) cc_final: 0.8724 (t) REVERT: A 1013 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 1179 MET cc_start: 0.8921 (tpp) cc_final: 0.8710 (tpp) REVERT: A 1230 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8205 (t0) REVERT: A 1310 PHE cc_start: 0.7147 (m-80) cc_final: 0.6870 (m-80) REVERT: A 1324 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8651 (pp30) REVERT: A 1402 LEU cc_start: 0.9123 (mt) cc_final: 0.8869 (tt) REVERT: A 1462 ASN cc_start: 0.9318 (m-40) cc_final: 0.9015 (p0) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 0.1004 time to fit residues: 23.6497 Evaluate side-chains 150 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN A1267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102093 restraints weight = 20111.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097879 restraints weight = 18433.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098574 restraints weight = 15847.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099034 restraints weight = 12569.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099297 restraints weight = 11249.299| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11486 Z= 0.108 Angle : 0.575 9.704 15593 Z= 0.285 Chirality : 0.041 0.142 1787 Planarity : 0.003 0.056 1968 Dihedral : 5.032 19.818 1544 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.96 % Allowed : 12.80 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -2.10 (0.22), residues: 1416 helix: -1.44 (0.17), residues: 876 sheet: -0.02 (0.70), residues: 68 loop : -1.15 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.014 0.001 TYR A 369 PHE 0.020 0.001 PHE A 832 TRP 0.017 0.001 TRP A 265 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00243 (11485) covalent geometry : angle 0.57508 (15591) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.47200 ( 2) hydrogen bonds : bond 0.03539 ( 379) hydrogen bonds : angle 4.51462 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.7981 (m-80) cc_final: 0.7617 (t80) REVERT: A 149 TYR cc_start: 0.8813 (t80) cc_final: 0.8319 (t80) REVERT: A 228 GLU cc_start: 0.7456 (tt0) cc_final: 0.6804 (pt0) REVERT: A 666 LEU cc_start: 0.8674 (mt) cc_final: 0.8000 (mt) REVERT: A 702 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 792 ARG cc_start: 0.7854 (mpp80) cc_final: 0.7337 (mtm180) REVERT: A 919 TRP cc_start: 0.7544 (t60) cc_final: 0.7192 (t60) REVERT: A 923 MET cc_start: 0.7755 (tpp) cc_final: 0.7409 (tpt) REVERT: A 999 SER cc_start: 0.9231 (m) cc_final: 0.8857 (t) REVERT: A 1013 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8022 (tt) REVERT: A 1046 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 1126 MET cc_start: 0.8725 (tpt) cc_final: 0.8256 (tpt) REVERT: A 1310 PHE cc_start: 0.7033 (m-80) cc_final: 0.6814 (m-80) REVERT: A 1324 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8765 (pp30) REVERT: A 1402 LEU cc_start: 0.9139 (mt) cc_final: 0.8923 (tt) REVERT: A 1462 ASN cc_start: 0.9290 (m-40) cc_final: 0.8950 (p0) outliers start: 24 outliers final: 14 residues processed: 155 average time/residue: 0.1074 time to fit residues: 24.2015 Evaluate side-chains 150 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 101 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 GLN A1078 GLN A1230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102625 restraints weight = 20518.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099551 restraints weight = 15853.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100293 restraints weight = 14653.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100586 restraints weight = 11541.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100937 restraints weight = 10484.906| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11486 Z= 0.227 Angle : 0.677 12.195 15593 Z= 0.335 Chirality : 0.046 0.149 1787 Planarity : 0.004 0.059 1968 Dihedral : 5.309 21.844 1544 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.18 % Allowed : 13.53 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.96 (0.22), residues: 1416 helix: -1.31 (0.17), residues: 876 sheet: -0.10 (0.69), residues: 68 loop : -1.10 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.026 0.002 TYR A 369 PHE 0.021 0.002 PHE A 832 TRP 0.018 0.002 TRP A 265 HIS 0.005 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00525 (11485) covalent geometry : angle 0.67694 (15591) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.67886 ( 2) hydrogen bonds : bond 0.04241 ( 379) hydrogen bonds : angle 4.87093 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8615 (m) cc_final: 0.8068 (t) REVERT: A 145 PHE cc_start: 0.8073 (m-80) cc_final: 0.7793 (t80) REVERT: A 282 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 535 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 571 PHE cc_start: 0.6174 (t80) cc_final: 0.5495 (t80) REVERT: A 666 LEU cc_start: 0.8595 (mt) cc_final: 0.8183 (mt) REVERT: A 702 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8308 (p) REVERT: A 750 MET cc_start: 0.8851 (mmm) cc_final: 0.8296 (mmm) REVERT: A 787 LEU cc_start: 0.8833 (mp) cc_final: 0.8253 (mp) REVERT: A 792 ARG cc_start: 0.7879 (mpp80) cc_final: 0.7435 (mtm180) REVERT: A 919 TRP cc_start: 0.7696 (t60) cc_final: 0.7379 (t60) REVERT: A 930 LEU cc_start: 0.9166 (tp) cc_final: 0.8563 (tt) REVERT: A 999 SER cc_start: 0.9222 (m) cc_final: 0.8829 (t) REVERT: A 1013 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 1046 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9008 (mp) REVERT: A 1077 TYR cc_start: 0.9460 (OUTLIER) cc_final: 0.7557 (t80) REVERT: A 1118 MET cc_start: 0.9032 (mmm) cc_final: 0.8543 (mmm) REVERT: A 1230 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8126 (t0) REVERT: A 1310 PHE cc_start: 0.6896 (m-80) cc_final: 0.6674 (m-10) REVERT: A 1414 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8193 (p0) REVERT: A 1462 ASN cc_start: 0.9209 (m-40) cc_final: 0.8957 (p0) outliers start: 39 outliers final: 24 residues processed: 165 average time/residue: 0.1026 time to fit residues: 24.5740 Evaluate side-chains 165 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1171 ASN ** A1343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104103 restraints weight = 20376.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100386 restraints weight = 15013.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100988 restraints weight = 14729.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101493 restraints weight = 11405.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101841 restraints weight = 10219.343| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11486 Z= 0.156 Angle : 0.613 10.151 15593 Z= 0.303 Chirality : 0.043 0.138 1787 Planarity : 0.004 0.057 1968 Dihedral : 5.092 21.228 1544 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.61 % Allowed : 14.59 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.69 (0.22), residues: 1416 helix: -1.11 (0.17), residues: 875 sheet: -0.07 (0.68), residues: 68 loop : -0.94 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1231 TYR 0.020 0.001 TYR A 369 PHE 0.022 0.001 PHE A 90 TRP 0.018 0.001 TRP A 265 HIS 0.016 0.001 HIS A1343 Details of bonding type rmsd covalent geometry : bond 0.00366 (11485) covalent geometry : angle 0.61341 (15591) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.57757 ( 2) hydrogen bonds : bond 0.03776 ( 379) hydrogen bonds : angle 4.58718 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8056 (m-80) cc_final: 0.7775 (t80) REVERT: A 282 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: A 402 LEU cc_start: 0.7830 (mt) cc_final: 0.7173 (mp) REVERT: A 535 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8481 (tt) REVERT: A 571 PHE cc_start: 0.6063 (t80) cc_final: 0.5360 (t80) REVERT: A 666 LEU cc_start: 0.8657 (mt) cc_final: 0.8213 (mt) REVERT: A 698 ILE cc_start: 0.8811 (mm) cc_final: 0.8599 (mt) REVERT: A 702 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 750 MET cc_start: 0.8910 (mmm) cc_final: 0.8354 (mmm) REVERT: A 787 LEU cc_start: 0.8879 (mp) cc_final: 0.8303 (mp) REVERT: A 792 ARG cc_start: 0.7855 (mpp80) cc_final: 0.7411 (mtm180) REVERT: A 919 TRP cc_start: 0.7651 (t60) cc_final: 0.7317 (t60) REVERT: A 930 LEU cc_start: 0.9131 (tp) cc_final: 0.8529 (tt) REVERT: A 999 SER cc_start: 0.9184 (m) cc_final: 0.8793 (t) REVERT: A 1013 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 1046 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 1077 TYR cc_start: 0.9433 (OUTLIER) cc_final: 0.7420 (t80) REVERT: A 1310 PHE cc_start: 0.7084 (m-80) cc_final: 0.6708 (m-10) REVERT: A 1324 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 1337 LEU cc_start: 0.9166 (tp) cc_final: 0.8919 (tp) REVERT: A 1414 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8207 (p0) REVERT: A 1462 ASN cc_start: 0.9273 (m-40) cc_final: 0.8929 (p0) outliers start: 32 outliers final: 21 residues processed: 160 average time/residue: 0.1001 time to fit residues: 23.5404 Evaluate side-chains 159 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 39 optimal weight: 0.0470 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107479 restraints weight = 20332.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104371 restraints weight = 15271.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105165 restraints weight = 14408.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105640 restraints weight = 10895.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105977 restraints weight = 9827.963| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11486 Z= 0.100 Angle : 0.569 10.618 15593 Z= 0.280 Chirality : 0.040 0.144 1787 Planarity : 0.003 0.053 1968 Dihedral : 4.648 20.231 1544 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.47 % Allowed : 15.24 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.40 (0.23), residues: 1416 helix: -0.88 (0.18), residues: 880 sheet: 0.33 (0.74), residues: 58 loop : -0.85 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.013 0.001 TYR A 73 PHE 0.028 0.001 PHE A 832 TRP 0.018 0.001 TRP A 265 HIS 0.009 0.001 HIS A1343 Details of bonding type rmsd covalent geometry : bond 0.00223 (11485) covalent geometry : angle 0.56948 (15591) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.53009 ( 2) hydrogen bonds : bond 0.03169 ( 379) hydrogen bonds : angle 4.18873 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.7994 (m-80) cc_final: 0.7452 (t80) REVERT: A 666 LEU cc_start: 0.8588 (mt) cc_final: 0.7923 (mt) REVERT: A 702 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 750 MET cc_start: 0.8926 (mmm) cc_final: 0.8357 (mmm) REVERT: A 919 TRP cc_start: 0.7573 (t60) cc_final: 0.7245 (t60) REVERT: A 999 SER cc_start: 0.9117 (m) cc_final: 0.8803 (t) REVERT: A 1013 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 1046 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8837 (mp) REVERT: A 1077 TYR cc_start: 0.9422 (OUTLIER) cc_final: 0.7208 (t80) REVERT: A 1310 PHE cc_start: 0.6999 (m-80) cc_final: 0.6576 (m-10) REVERT: A 1324 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8710 (pp30) REVERT: A 1337 LEU cc_start: 0.9194 (tp) cc_final: 0.8926 (tt) REVERT: A 1394 LEU cc_start: 0.8747 (tt) cc_final: 0.8501 (tt) REVERT: A 1414 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 1462 ASN cc_start: 0.9289 (m-40) cc_final: 0.8900 (p0) outliers start: 18 outliers final: 9 residues processed: 150 average time/residue: 0.1007 time to fit residues: 21.7550 Evaluate side-chains 143 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101084 restraints weight = 19921.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097111 restraints weight = 20020.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097616 restraints weight = 19344.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098140 restraints weight = 14256.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098466 restraints weight = 12603.309| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11486 Z= 0.159 Angle : 0.623 10.874 15593 Z= 0.304 Chirality : 0.043 0.160 1787 Planarity : 0.004 0.050 1968 Dihedral : 4.741 20.466 1544 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.71 % Allowed : 15.40 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.36 (0.23), residues: 1416 helix: -0.85 (0.18), residues: 872 sheet: 0.17 (0.73), residues: 60 loop : -0.80 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1363 TYR 0.027 0.001 TYR A1096 PHE 0.023 0.001 PHE A 90 TRP 0.016 0.001 TRP A 265 HIS 0.003 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00371 (11485) covalent geometry : angle 0.62291 (15591) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.77968 ( 2) hydrogen bonds : bond 0.03590 ( 379) hydrogen bonds : angle 4.43630 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8082 (m-80) cc_final: 0.7551 (t80) REVERT: A 571 PHE cc_start: 0.6018 (t80) cc_final: 0.5335 (t80) REVERT: A 666 LEU cc_start: 0.8547 (mt) cc_final: 0.8088 (mt) REVERT: A 702 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 750 MET cc_start: 0.8786 (mmm) cc_final: 0.8268 (mmm) REVERT: A 919 TRP cc_start: 0.7642 (t60) cc_final: 0.7313 (t60) REVERT: A 930 LEU cc_start: 0.9069 (tp) cc_final: 0.8484 (tt) REVERT: A 999 SER cc_start: 0.9173 (m) cc_final: 0.8857 (t) REVERT: A 1013 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 1046 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 1077 TYR cc_start: 0.9438 (OUTLIER) cc_final: 0.7511 (t80) REVERT: A 1179 MET cc_start: 0.8892 (tpp) cc_final: 0.8542 (tpp) REVERT: A 1310 PHE cc_start: 0.6872 (m-80) cc_final: 0.6521 (m-10) REVERT: A 1324 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8711 (pp30) REVERT: A 1337 LEU cc_start: 0.9202 (tp) cc_final: 0.8933 (tt) REVERT: A 1414 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8149 (p0) REVERT: A 1462 ASN cc_start: 0.9211 (m-40) cc_final: 0.8831 (p0) REVERT: A 1474 MET cc_start: 0.8751 (mmp) cc_final: 0.7939 (mtm) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.1120 time to fit residues: 23.2973 Evaluate side-chains 144 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 0.0870 chunk 57 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101155 restraints weight = 20067.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100328 restraints weight = 18556.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100264 restraints weight = 17332.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100765 restraints weight = 12783.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101543 restraints weight = 10861.379| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11486 Z= 0.116 Angle : 0.616 12.718 15593 Z= 0.299 Chirality : 0.042 0.206 1787 Planarity : 0.003 0.047 1968 Dihedral : 4.608 20.973 1544 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.63 % Allowed : 15.65 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.22 (0.23), residues: 1416 helix: -0.68 (0.18), residues: 864 sheet: 0.07 (0.72), residues: 60 loop : -0.85 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 807 TYR 0.016 0.001 TYR A1096 PHE 0.023 0.001 PHE A 90 TRP 0.018 0.001 TRP A 265 HIS 0.003 0.001 HIS A1435 Details of bonding type rmsd covalent geometry : bond 0.00274 (11485) covalent geometry : angle 0.61576 (15591) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.74503 ( 2) hydrogen bonds : bond 0.03351 ( 379) hydrogen bonds : angle 4.29510 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8077 (m-80) cc_final: 0.7538 (t80) REVERT: A 571 PHE cc_start: 0.5990 (t80) cc_final: 0.5182 (t80) REVERT: A 572 MET cc_start: 0.7456 (mmm) cc_final: 0.7009 (mmm) REVERT: A 666 LEU cc_start: 0.8539 (mt) cc_final: 0.7881 (mt) REVERT: A 698 ILE cc_start: 0.8814 (mm) cc_final: 0.8607 (mt) REVERT: A 702 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 750 MET cc_start: 0.8866 (mmm) cc_final: 0.8351 (mmm) REVERT: A 792 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7438 (mtm-85) REVERT: A 919 TRP cc_start: 0.7596 (t60) cc_final: 0.7270 (t60) REVERT: A 930 LEU cc_start: 0.8988 (tp) cc_final: 0.8380 (tt) REVERT: A 999 SER cc_start: 0.9182 (m) cc_final: 0.8954 (t) REVERT: A 1013 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 1046 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8815 (mp) REVERT: A 1077 TYR cc_start: 0.9400 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 1179 MET cc_start: 0.8966 (tpp) cc_final: 0.8643 (tpp) REVERT: A 1310 PHE cc_start: 0.6849 (m-80) cc_final: 0.6528 (m-80) REVERT: A 1324 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 1337 LEU cc_start: 0.9188 (tp) cc_final: 0.8871 (tt) REVERT: A 1414 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8155 (p0) REVERT: A 1462 ASN cc_start: 0.9221 (m-40) cc_final: 0.8846 (p0) outliers start: 20 outliers final: 15 residues processed: 140 average time/residue: 0.0908 time to fit residues: 18.8146 Evaluate side-chains 145 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 58 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.149478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103088 restraints weight = 19920.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099273 restraints weight = 15413.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100061 restraints weight = 13802.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100619 restraints weight = 10523.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100863 restraints weight = 9292.618| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11486 Z= 0.101 Angle : 0.607 12.033 15593 Z= 0.294 Chirality : 0.041 0.177 1787 Planarity : 0.003 0.044 1968 Dihedral : 4.429 20.625 1544 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.63 % Allowed : 15.73 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.10 (0.23), residues: 1416 helix: -0.54 (0.18), residues: 860 sheet: 0.08 (0.71), residues: 60 loop : -0.89 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1362 TYR 0.014 0.001 TYR A 135 PHE 0.023 0.001 PHE A 90 TRP 0.017 0.001 TRP A 265 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00237 (11485) covalent geometry : angle 0.60695 (15591) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.77187 ( 2) hydrogen bonds : bond 0.03067 ( 379) hydrogen bonds : angle 4.11475 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.58 seconds wall clock time: 30 minutes 46.43 seconds (1846.43 seconds total)