Starting phenix.real_space_refine on Fri Jul 3 04:12:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.cif" model { file = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usm_26739/07_2026/7usm_26739.map" } resolution = 2.7 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= 0.012 sd= 1.262 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 98 5.16 5 C 7386 2.51 5 N 2092 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11893 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6559 Classifications: {'peptide': 848} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 808} Chain breaks: 4 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5176 Classifications: {'peptide': 673} Link IDs: {'PCIS': 4, 'PTRANS': 31, 'TRANS': 637} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 115 Unusual residues: {' CA': 3, 'NAG': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11893 At special positions: 0 Unit cell: (122.322, 121.249, 127.687, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 98 16.00 O 2313 8.00 N 2092 7.00 C 7386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1016 " distance=2.03 Simple disulfide: pdb=" SG CYS A1006 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 519 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 625 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 673 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1204 " - " ASN A1034 " " NAG A1205 " - " ASN A 70 " " NAG A1206 " - " ASN A 718 " " NAG A1207 " - " ASN A 785 " " NAG A1208 " - " ASN A 864 " " NAG A1209 " - " ASN A 884 " " NAG A1210 " - " ASN A1005 " " NAG A1211 " - " ASN A1028 " " NAG B 802 " - " ASN B 94 " " NAG C 1 " - " ASN A 375 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 32 sheets defined 14.7% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.642A pdb=" N PHE A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.933A pdb=" N LEU A 998 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.638A pdb=" N ALA A1071 " --> pdb=" O GLY A1068 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A1072 " --> pdb=" O GLN A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1068 through 1072' Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.546A pdb=" N CYS B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 15 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.977A pdb=" N THR B 30 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.589A pdb=" N ARG B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.665A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.760A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.686A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 301 through 315 removed outlier: 4.582A pdb=" N LYS B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.733A pdb=" N LEU B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.819A pdb=" N SER B 569 " --> pdb=" O VAL B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 4.290A pdb=" N GLY B 601 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.494A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.891A pdb=" N MET A 9 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.875A pdb=" N ARG A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 58 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 56 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 removed outlier: 7.160A pdb=" N GLN A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.896A pdb=" N SER A 76 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 397 removed outlier: 8.370A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 416 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 431 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET A 418 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 425 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 5.987A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 491 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.607A pdb=" N GLN A 553 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 removed outlier: 4.153A pdb=" N GLU A 631 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 689 Processing sheet with id=AB3, first strand: chain 'A' and resid 765 through 769 removed outlier: 3.751A pdb=" N SER A 769 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 866 " --> pdb=" O ARG A 813 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 797 through 798 removed outlier: 3.538A pdb=" N SER A 797 " --> pdb=" O PHE A 855 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 832 removed outlier: 4.435A pdb=" N LEU A 881 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 901 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 907 through 908 removed outlier: 6.346A pdb=" N TYR A 907 " --> pdb=" O THR A1064 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 911 through 914 removed outlier: 3.724A pdb=" N GLY A1033 " --> pdb=" O MET A 935 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 937 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A1029 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 922 through 923 removed outlier: 13.196A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A1020 " --> pdb=" O PRO A 950 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER A 952 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A1018 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL A 954 " --> pdb=" O CYS A1016 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS A1016 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU A 956 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A1014 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN A1012 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 981 " --> pdb=" O ASP A1017 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.574A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 13.196A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.787A pdb=" N LEU B 62 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 80 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 76 through 77 removed outlier: 4.014A pdb=" N THR B 388 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 394 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 182 through 189 removed outlier: 7.066A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE B 146 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC7, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AC8, first strand: chain 'B' and resid 507 through 508 Processing sheet with id=AC9, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 533 through 536 Processing sheet with id=AD2, first strand: chain 'B' and resid 546 through 547 Processing sheet with id=AD3, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.564A pdb=" N VAL B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 629 through 630 removed outlier: 3.550A pdb=" N TYR B 666 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 642 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 638 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 629 through 630 removed outlier: 3.550A pdb=" N TYR B 666 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 672 " --> pdb=" O TRP B 649 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1002 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: 2.87 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4028 1.34 - 1.46: 2635 1.46 - 1.58: 5332 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 12114 Sorted by residual: bond pdb=" C1 NAG A1207 " pdb=" O5 NAG A1207 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 NAG A1211 " pdb=" O5 NAG A1211 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG A1205 " pdb=" O5 NAG A1205 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG A1206 " pdb=" O5 NAG A1206 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 12109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 15947 1.71 - 3.43: 405 3.43 - 5.14: 42 5.14 - 6.86: 7 6.86 - 8.57: 4 Bond angle restraints: 16405 Sorted by residual: angle pdb=" N LEU B 443 " pdb=" CA LEU B 443 " pdb=" C LEU B 443 " ideal model delta sigma weight residual 108.73 115.67 -6.94 1.63e+00 3.76e-01 1.81e+01 angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 114.40 118.00 -3.60 1.11e+00 8.12e-01 1.05e+01 angle pdb=" N GLU B 444 " pdb=" CA GLU B 444 " pdb=" CB GLU B 444 " ideal model delta sigma weight residual 111.13 116.75 -5.62 1.79e+00 3.12e-01 9.87e+00 angle pdb=" C PHE B 442 " pdb=" CA PHE B 442 " pdb=" CB PHE B 442 " ideal model delta sigma weight residual 109.38 115.35 -5.97 2.03e+00 2.43e-01 8.65e+00 angle pdb=" N LYS B 5 " pdb=" CA LYS B 5 " pdb=" C LYS B 5 " ideal model delta sigma weight residual 108.41 112.63 -4.22 1.63e+00 3.76e-01 6.69e+00 ... (remaining 16400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6757 17.95 - 35.91: 452 35.91 - 53.86: 67 53.86 - 71.81: 23 71.81 - 89.77: 12 Dihedral angle restraints: 7311 sinusoidal: 2965 harmonic: 4346 Sorted by residual: dihedral pdb=" CB CYS B 593 " pdb=" SG CYS B 593 " pdb=" SG CYS B 596 " pdb=" CB CYS B 596 " ideal model delta sinusoidal sigma weight residual -86.00 -167.73 81.73 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 540 " pdb=" CB CYS B 540 " ideal model delta sinusoidal sigma weight residual 93.00 160.09 -67.09 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS B 497 " pdb=" SG CYS B 497 " pdb=" SG CYS B 512 " pdb=" CB CYS B 512 " ideal model delta sinusoidal sigma weight residual 93.00 151.69 -58.69 1 1.00e+01 1.00e-02 4.61e+01 ... (remaining 7308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1322 0.042 - 0.084: 370 0.084 - 0.126: 147 0.126 - 0.168: 12 0.168 - 0.210: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CB VAL B 233 " pdb=" CA VAL B 233 " pdb=" CG1 VAL B 233 " pdb=" CG2 VAL B 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA GLU B 444 " pdb=" N GLU B 444 " pdb=" C GLU B 444 " pdb=" CB GLU B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1851 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 373 " -0.062 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 374 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 374 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 374 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 529 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 530 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 530 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 530 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 385 " -0.051 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 386 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.042 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 197 2.67 - 3.23: 11157 3.23 - 3.78: 17180 3.78 - 4.34: 24208 4.34 - 4.90: 40055 Nonbonded interactions: 92797 Sorted by model distance: nonbonded pdb=" OG1 THR B 258 " pdb=" O GLU B 276 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASP B 243 " pdb=" N GLY B 244 " model vdw 2.116 3.120 nonbonded pdb=" OG SER A 21 " pdb=" O GLY A 74 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR B 603 " pdb=" OD1 ASP B 661 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR A 470 " pdb=" OE1 GLN A 497 " model vdw 2.217 3.040 ... (remaining 92792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12153 Z= 0.140 Angle : 0.640 8.572 16494 Z= 0.329 Chirality : 0.045 0.210 1854 Planarity : 0.006 0.093 2162 Dihedral : 12.765 89.769 4437 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1509 helix: -1.69 (0.39), residues: 157 sheet: 0.48 (0.24), residues: 466 loop : -0.97 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 409 TYR 0.021 0.002 TYR A 440 PHE 0.026 0.002 PHE B 149 TRP 0.024 0.002 TRP B 230 HIS 0.004 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12114) covalent geometry : angle 0.63126 / 0.33 (16405) SS BOND : bond 0.00208 / 0.12 ( 28) SS BOND : angle 0.91798 / 0.63 ( 56) hydrogen bonds : bond 0.25077 / 16.75 ( 378) hydrogen bonds : angle 9.70172 / 6.64 ( 1002) link_BETA1-4 : bond 0.00199 / 0.10 ( 1) link_BETA1-4 : angle 1.25696 / 0.87 ( 3) link_NAG-ASN : bond 0.00169 / 0.08 ( 10) link_NAG-ASN : angle 2.30397 / 1.47 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.454 Fit side-chains REVERT: A 470 THR cc_start: 0.8014 (p) cc_final: 0.7806 (p) REVERT: A 681 SER cc_start: 0.7420 (p) cc_final: 0.7204 (t) REVERT: B 115 TYR cc_start: 0.6654 (t80) cc_final: 0.6433 (t80) REVERT: B 309 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.6181 time to fit residues: 155.4751 Evaluate side-chains 192 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN A 852 HIS A 895 ASN A 916 HIS ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 657 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.177718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156105 restraints weight = 15893.884| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.27 r_work: 0.4018 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12153 Z= 0.214 Angle : 0.695 8.902 16494 Z= 0.362 Chirality : 0.047 0.176 1854 Planarity : 0.006 0.067 2162 Dihedral : 5.423 22.139 1644 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.21 % Allowed : 8.59 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1509 helix: -1.14 (0.40), residues: 151 sheet: 0.56 (0.24), residues: 478 loop : -0.84 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 636 TYR 0.016 0.002 TYR B 279 PHE 0.024 0.003 PHE B 442 TRP 0.015 0.002 TRP A1039 HIS 0.009 0.002 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (12114) covalent geometry : angle 0.68407 / 0.36 (16405) SS BOND : bond 0.00332 / 0.19 ( 28) SS BOND : angle 1.10879 / 0.83 ( 56) hydrogen bonds : bond 0.04983 / 3.36 ( 378) hydrogen bonds : angle 7.26665 / 4.99 ( 1002) link_BETA1-4 : bond 0.00547 / 0.29 ( 1) link_BETA1-4 : angle 2.22904 / 1.34 ( 3) link_NAG-ASN : bond 0.00378 / 0.19 ( 10) link_NAG-ASN : angle 2.58698 / 1.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8034 (ptt180) cc_final: 0.7642 (pmm-80) REVERT: A 346 ASN cc_start: 0.7474 (p0) cc_final: 0.7229 (t0) REVERT: A 470 THR cc_start: 0.8170 (p) cc_final: 0.7910 (p) REVERT: B 64 GLU cc_start: 0.5564 (mp0) cc_final: 0.4985 (mp0) REVERT: B 202 GLN cc_start: 0.7249 (mm110) cc_final: 0.6988 (mm-40) REVERT: B 273 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7355 (mtp85) REVERT: B 276 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: B 295 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7739 (mt0) outliers start: 29 outliers final: 14 residues processed: 241 average time/residue: 0.6297 time to fit residues: 164.3358 Evaluate side-chains 221 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.0000 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 143 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 106 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 575 GLN A 676 ASN A 701 GLN A 895 ASN A 916 HIS B 184 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.179787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.158330 restraints weight = 16112.227| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.30 r_work: 0.4047 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12153 Z= 0.134 Angle : 0.625 8.905 16494 Z= 0.327 Chirality : 0.045 0.200 1854 Planarity : 0.005 0.059 2162 Dihedral : 5.099 22.214 1644 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 13.00 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1509 helix: -0.95 (0.42), residues: 150 sheet: 0.57 (0.23), residues: 481 loop : -0.78 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 636 TYR 0.011 0.001 TYR B 279 PHE 0.022 0.002 PHE A1072 TRP 0.011 0.002 TRP A1039 HIS 0.005 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12114) covalent geometry : angle 0.61132 / 0.32 (16405) SS BOND : bond 0.00493 / 0.25 ( 28) SS BOND : angle 1.50427 / 1.15 ( 56) hydrogen bonds : bond 0.03938 / 2.64 ( 378) hydrogen bonds : angle 6.63360 / 4.58 ( 1002) link_BETA1-4 : bond 0.00094 / 0.05 ( 1) link_BETA1-4 : angle 1.49096 / 0.93 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 10) link_NAG-ASN : angle 2.38907 / 1.50 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7577 (pmm-80) REVERT: A 346 ASN cc_start: 0.7416 (p0) cc_final: 0.7216 (t0) REVERT: A 470 THR cc_start: 0.8158 (p) cc_final: 0.7895 (p) REVERT: A 1035 LEU cc_start: 0.6429 (tp) cc_final: 0.6197 (tp) REVERT: B 25 GLN cc_start: 0.6132 (mp-120) cc_final: 0.5358 (mp10) REVERT: B 64 GLU cc_start: 0.5480 (mp0) cc_final: 0.4912 (mp0) REVERT: B 202 GLN cc_start: 0.7309 (mm110) cc_final: 0.7015 (mm-40) REVERT: B 212 GLU cc_start: 0.6331 (mp0) cc_final: 0.6083 (mp0) REVERT: B 226 GLU cc_start: 0.6864 (pm20) cc_final: 0.6608 (pm20) REVERT: B 295 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: B 359 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7705 (p) outliers start: 33 outliers final: 9 residues processed: 235 average time/residue: 0.6495 time to fit residues: 164.8114 Evaluate side-chains 208 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 657 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 141 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN A 701 GLN A 895 ASN B 518 ASN B 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.177913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.156459 restraints weight = 15998.860| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.26 r_work: 0.4023 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12153 Z= 0.190 Angle : 0.663 13.168 16494 Z= 0.345 Chirality : 0.046 0.238 1854 Planarity : 0.005 0.057 2162 Dihedral : 5.225 23.136 1644 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.04 % Allowed : 14.75 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1509 helix: -1.04 (0.41), residues: 157 sheet: 0.49 (0.23), residues: 495 loop : -0.85 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 636 TYR 0.015 0.002 TYR B 279 PHE 0.030 0.003 PHE B 146 TRP 0.013 0.002 TRP A1039 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (12114) covalent geometry : angle 0.64948 / 0.34 (16405) SS BOND : bond 0.00489 / 0.25 ( 28) SS BOND : angle 1.44043 / 1.18 ( 56) hydrogen bonds : bond 0.04052 / 2.70 ( 378) hydrogen bonds : angle 6.55057 / 4.52 ( 1002) link_BETA1-4 : bond 0.00323 / 0.17 ( 1) link_BETA1-4 : angle 2.23914 / 1.47 ( 3) link_NAG-ASN : bond 0.00302 / 0.14 ( 10) link_NAG-ASN : angle 2.58551 / 1.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7979 (ptt180) cc_final: 0.7663 (pmm-80) REVERT: A 346 ASN cc_start: 0.7477 (p0) cc_final: 0.7248 (t0) REVERT: A 716 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7257 (ttm110) REVERT: A 1035 LEU cc_start: 0.6474 (tp) cc_final: 0.6223 (tp) REVERT: B 25 GLN cc_start: 0.6002 (mp-120) cc_final: 0.5460 (mp-120) REVERT: B 64 GLU cc_start: 0.5509 (mp0) cc_final: 0.4966 (mp0) REVERT: B 226 GLU cc_start: 0.6897 (pm20) cc_final: 0.6630 (pm20) REVERT: B 264 CYS cc_start: 0.6243 (t) cc_final: 0.5919 (t) REVERT: B 276 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: B 359 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7717 (m) REVERT: B 521 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7767 (mtt-85) outliers start: 40 outliers final: 18 residues processed: 226 average time/residue: 0.5828 time to fit residues: 143.4495 Evaluate side-chains 216 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 133 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 82 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.0060 chunk 93 optimal weight: 1.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN A 701 GLN A 895 ASN B 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.178052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156587 restraints weight = 15965.672| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.28 r_work: 0.4026 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12153 Z= 0.167 Angle : 0.649 11.522 16494 Z= 0.337 Chirality : 0.046 0.214 1854 Planarity : 0.005 0.050 2162 Dihedral : 5.189 23.670 1644 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.57 % Allowed : 15.89 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1509 helix: -0.98 (0.42), residues: 151 sheet: 0.45 (0.23), residues: 483 loop : -0.84 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 636 TYR 0.014 0.001 TYR B 279 PHE 0.030 0.002 PHE B 149 TRP 0.012 0.002 TRP A1039 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (12114) covalent geometry : angle 0.63657 / 0.33 (16405) SS BOND : bond 0.00444 / 0.23 ( 28) SS BOND : angle 1.38008 / 1.11 ( 56) hydrogen bonds : bond 0.03807 / 2.54 ( 378) hydrogen bonds : angle 6.45394 / 4.44 ( 1002) link_BETA1-4 : bond 0.00118 / 0.06 ( 1) link_BETA1-4 : angle 2.06116 / 1.38 ( 3) link_NAG-ASN : bond 0.00250 / 0.11 ( 10) link_NAG-ASN : angle 2.40308 / 1.51 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7989 (ptt180) cc_final: 0.7690 (pmm-80) REVERT: A 346 ASN cc_start: 0.7419 (p0) cc_final: 0.7211 (t0) REVERT: A 681 SER cc_start: 0.7791 (p) cc_final: 0.7537 (t) REVERT: B 25 GLN cc_start: 0.6010 (mp-120) cc_final: 0.5344 (mp10) REVERT: B 64 GLU cc_start: 0.5436 (mp0) cc_final: 0.4920 (mp0) REVERT: B 212 GLU cc_start: 0.6416 (mp0) cc_final: 0.6135 (mp0) REVERT: B 226 GLU cc_start: 0.6917 (pm20) cc_final: 0.6641 (pm20) REVERT: B 276 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: B 295 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 359 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (m) REVERT: B 390 GLN cc_start: 0.8101 (mt0) cc_final: 0.7873 (mt0) REVERT: B 521 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: B 660 MET cc_start: 0.6564 (tmm) cc_final: 0.6288 (tmm) REVERT: B 662 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6989 (ttp-170) outliers start: 47 outliers final: 18 residues processed: 236 average time/residue: 0.5892 time to fit residues: 151.1972 Evaluate side-chains 221 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN A 701 GLN A 851 ASN A 895 ASN B 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.177310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155830 restraints weight = 15998.688| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.28 r_work: 0.4018 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12153 Z= 0.184 Angle : 0.668 11.290 16494 Z= 0.348 Chirality : 0.046 0.221 1854 Planarity : 0.005 0.047 2162 Dihedral : 5.301 23.542 1644 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.73 % Allowed : 16.65 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1509 helix: -0.89 (0.42), residues: 151 sheet: 0.44 (0.23), residues: 491 loop : -0.85 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 893 TYR 0.014 0.001 TYR B 279 PHE 0.036 0.002 PHE B 149 TRP 0.012 0.002 TRP A1039 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (12114) covalent geometry : angle 0.65290 / 0.34 (16405) SS BOND : bond 0.00462 / 0.25 ( 28) SS BOND : angle 1.62594 / 1.38 ( 56) hydrogen bonds : bond 0.03901 / 2.59 ( 378) hydrogen bonds : angle 6.46388 / 4.45 ( 1002) link_BETA1-4 : bond 0.00330 / 0.17 ( 1) link_BETA1-4 : angle 2.23902 / 1.44 ( 3) link_NAG-ASN : bond 0.00321 / 0.15 ( 10) link_NAG-ASN : angle 2.55156 / 1.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7771 (pmm-80) REVERT: A 346 ASN cc_start: 0.7422 (p0) cc_final: 0.7213 (t0) REVERT: A 376 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.4531 (mtt) REVERT: A 681 SER cc_start: 0.7789 (p) cc_final: 0.7555 (t) REVERT: B 25 GLN cc_start: 0.5997 (mp-120) cc_final: 0.5531 (mp-120) REVERT: B 64 GLU cc_start: 0.5334 (mp0) cc_final: 0.4837 (mp0) REVERT: B 226 GLU cc_start: 0.6935 (pm20) cc_final: 0.6641 (pm20) REVERT: B 276 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: B 295 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: B 521 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7642 (mtt-85) REVERT: B 657 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: B 662 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6489 (ttp-170) outliers start: 49 outliers final: 27 residues processed: 231 average time/residue: 0.5968 time to fit residues: 150.0870 Evaluate side-chains 229 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN A 701 GLN A 895 ASN B 518 ASN B 582 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.177759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.156363 restraints weight = 15893.395| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.27 r_work: 0.4020 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12153 Z= 0.182 Angle : 0.678 11.768 16494 Z= 0.352 Chirality : 0.046 0.220 1854 Planarity : 0.005 0.050 2162 Dihedral : 5.363 30.879 1644 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.65 % Allowed : 17.95 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.22), residues: 1509 helix: -0.84 (0.42), residues: 145 sheet: 0.39 (0.24), residues: 479 loop : -0.87 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 893 TYR 0.014 0.001 TYR B 279 PHE 0.044 0.003 PHE B 149 TRP 0.012 0.002 TRP A1039 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (12114) covalent geometry : angle 0.66274 / 0.35 (16405) SS BOND : bond 0.00464 / 0.25 ( 28) SS BOND : angle 1.80352 / 1.40 ( 56) hydrogen bonds : bond 0.03824 / 2.55 ( 378) hydrogen bonds : angle 6.44420 / 4.43 ( 1002) link_BETA1-4 : bond 0.00298 / 0.16 ( 1) link_BETA1-4 : angle 2.18728 / 1.45 ( 3) link_NAG-ASN : bond 0.00323 / 0.15 ( 10) link_NAG-ASN : angle 2.47696 / 1.57 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8037 (ptt180) cc_final: 0.7785 (pmm-80) REVERT: A 376 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.4946 (mmt) REVERT: A 681 SER cc_start: 0.7793 (p) cc_final: 0.7578 (t) REVERT: A 716 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7325 (ttm110) REVERT: A 874 SER cc_start: 0.8809 (p) cc_final: 0.8609 (p) REVERT: B 25 GLN cc_start: 0.6032 (mp-120) cc_final: 0.5371 (mp10) REVERT: B 64 GLU cc_start: 0.5362 (mp0) cc_final: 0.4847 (mp0) REVERT: B 226 GLU cc_start: 0.6946 (pm20) cc_final: 0.6645 (pm20) REVERT: B 295 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: B 390 GLN cc_start: 0.8165 (mt0) cc_final: 0.7879 (mt0) REVERT: B 660 MET cc_start: 0.6939 (tpp) cc_final: 0.6679 (tpt) REVERT: B 662 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6576 (ttp-170) outliers start: 48 outliers final: 30 residues processed: 230 average time/residue: 0.6215 time to fit residues: 155.3636 Evaluate side-chains 230 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 851 ASN A 895 ASN B 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.177096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.155799 restraints weight = 15852.553| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.25 r_work: 0.4013 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12153 Z= 0.212 Angle : 0.709 10.874 16494 Z= 0.369 Chirality : 0.047 0.222 1854 Planarity : 0.005 0.069 2162 Dihedral : 5.488 30.277 1644 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.73 % Allowed : 17.79 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1509 helix: -0.82 (0.43), residues: 145 sheet: 0.32 (0.24), residues: 481 loop : -0.94 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 636 TYR 0.014 0.002 TYR B 279 PHE 0.050 0.003 PHE B 149 TRP 0.013 0.002 TRP A1039 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (12114) covalent geometry : angle 0.68904 / 0.36 (16405) SS BOND : bond 0.00454 / 0.25 ( 28) SS BOND : angle 2.28448 / 1.85 ( 56) hydrogen bonds : bond 0.04002 / 2.67 ( 378) hydrogen bonds : angle 6.52281 / 4.49 ( 1002) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 2.41213 / 1.55 ( 3) link_NAG-ASN : bond 0.00399 / 0.19 ( 10) link_NAG-ASN : angle 2.53664 / 1.62 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8041 (ptt180) cc_final: 0.7797 (pmm-80) REVERT: A 346 ASN cc_start: 0.7900 (t0) cc_final: 0.7637 (t0) REVERT: A 376 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5019 (mmt) REVERT: A 681 SER cc_start: 0.7837 (p) cc_final: 0.7628 (t) REVERT: A 716 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7294 (ttm110) REVERT: B 25 GLN cc_start: 0.6039 (mp-120) cc_final: 0.5570 (mp-120) REVERT: B 64 GLU cc_start: 0.5375 (mp0) cc_final: 0.4864 (mp0) REVERT: B 226 GLU cc_start: 0.6961 (pm20) cc_final: 0.6670 (pm20) REVERT: B 295 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: B 390 GLN cc_start: 0.8198 (mt0) cc_final: 0.7907 (mt0) REVERT: B 521 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7670 (mtt-85) REVERT: B 662 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7015 (ttp-170) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.5312 time to fit residues: 133.9061 Evaluate side-chains 236 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 701 GLN A 895 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.177406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.155683 restraints weight = 15773.252| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.31 r_work: 0.4018 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12153 Z= 0.178 Angle : 0.700 12.266 16494 Z= 0.362 Chirality : 0.046 0.222 1854 Planarity : 0.005 0.075 2162 Dihedral : 5.430 28.649 1644 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.51 % Allowed : 19.39 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1509 helix: -0.82 (0.43), residues: 145 sheet: 0.37 (0.24), residues: 486 loop : -0.99 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 636 TYR 0.013 0.001 TYR B 279 PHE 0.055 0.003 PHE B 149 TRP 0.012 0.002 TRP A1039 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (12114) covalent geometry : angle 0.68229 / 0.36 (16405) SS BOND : bond 0.00454 / 0.25 ( 28) SS BOND : angle 2.03889 / 1.59 ( 56) hydrogen bonds : bond 0.03816 / 2.54 ( 378) hydrogen bonds : angle 6.45891 / 4.45 ( 1002) link_BETA1-4 : bond 0.00239 / 0.13 ( 1) link_BETA1-4 : angle 2.14182 / 1.42 ( 3) link_NAG-ASN : bond 0.00284 / 0.13 ( 10) link_NAG-ASN : angle 2.50950 / 1.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8044 (ptt180) cc_final: 0.7733 (pmm-80) REVERT: A 716 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7245 (ttm110) REVERT: B 25 GLN cc_start: 0.6042 (mp-120) cc_final: 0.5567 (mp-120) REVERT: B 64 GLU cc_start: 0.5339 (mp0) cc_final: 0.4831 (mp0) REVERT: B 226 GLU cc_start: 0.6950 (pm20) cc_final: 0.6662 (pm20) REVERT: B 295 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: B 390 GLN cc_start: 0.8189 (mt0) cc_final: 0.7943 (mt0) REVERT: B 521 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7632 (mtt-85) REVERT: B 662 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6703 (ttp-170) outliers start: 33 outliers final: 27 residues processed: 226 average time/residue: 0.5310 time to fit residues: 130.5620 Evaluate side-chains 227 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.0070 chunk 117 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN A 701 GLN A 895 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.176757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.154987 restraints weight = 15957.406| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.32 r_work: 0.4015 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12153 Z= 0.194 Angle : 0.721 12.101 16494 Z= 0.371 Chirality : 0.046 0.219 1854 Planarity : 0.005 0.061 2162 Dihedral : 5.465 29.372 1644 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.43 % Allowed : 19.85 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1509 helix: -0.81 (0.43), residues: 145 sheet: 0.31 (0.24), residues: 486 loop : -1.00 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 893 TYR 0.014 0.001 TYR B 279 PHE 0.053 0.003 PHE B 149 TRP 0.013 0.002 TRP A1039 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (12114) covalent geometry : angle 0.70418 / 0.37 (16405) SS BOND : bond 0.00480 / 0.26 ( 28) SS BOND : angle 2.01044 / 1.55 ( 56) hydrogen bonds : bond 0.03924 / 2.62 ( 378) hydrogen bonds : angle 6.49675 / 4.47 ( 1002) link_BETA1-4 : bond 0.00358 / 0.19 ( 1) link_BETA1-4 : angle 2.19591 / 1.48 ( 3) link_NAG-ASN : bond 0.00376 / 0.18 ( 10) link_NAG-ASN : angle 2.50188 / 1.61 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8052 (ptt180) cc_final: 0.7756 (pmm-80) REVERT: A 716 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7278 (ttm110) REVERT: B 25 GLN cc_start: 0.6007 (mp-120) cc_final: 0.5533 (mp-120) REVERT: B 64 GLU cc_start: 0.5357 (mp0) cc_final: 0.4833 (mp0) REVERT: B 226 GLU cc_start: 0.6940 (pm20) cc_final: 0.6650 (pm20) REVERT: B 295 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: B 662 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7005 (ttp-170) outliers start: 32 outliers final: 27 residues processed: 217 average time/residue: 0.5034 time to fit residues: 118.8203 Evaluate side-chains 225 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 662 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 105 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 701 GLN A 851 ASN A 895 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.177102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.155534 restraints weight = 15938.143| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.31 r_work: 0.4019 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12153 Z= 0.182 Angle : 0.711 11.910 16494 Z= 0.366 Chirality : 0.046 0.206 1854 Planarity : 0.005 0.061 2162 Dihedral : 5.440 29.327 1644 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.81 % Allowed : 19.32 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.21), residues: 1509 helix: -0.79 (0.43), residues: 145 sheet: 0.32 (0.24), residues: 486 loop : -0.99 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 893 TYR 0.014 0.001 TYR B 279 PHE 0.053 0.003 PHE B 149 TRP 0.014 0.002 TRP A 501 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (12114) covalent geometry : angle 0.69705 / 0.36 (16405) SS BOND : bond 0.00470 / 0.25 ( 28) SS BOND : angle 1.87985 / 1.44 ( 56) hydrogen bonds : bond 0.03847 / 2.55 ( 378) hydrogen bonds : angle 6.46331 / 4.45 ( 1002) link_BETA1-4 : bond 0.00258 / 0.14 ( 1) link_BETA1-4 : angle 2.14113 / 1.43 ( 3) link_NAG-ASN : bond 0.00316 / 0.15 ( 10) link_NAG-ASN : angle 2.35674 / 1.49 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6632.56 seconds wall clock time: 113 minutes 28.46 seconds (6808.46 seconds total)