Starting phenix.real_space_refine on Tue Jul 7 01:45:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqs_18603/07_2026/8qqs_18603.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.186 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 S 76 5.16 5 C 13134 2.51 5 N 3770 2.21 5 O 4157 1.98 5 H 20715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 41912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 8280 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain: "B" Number of atoms: 11766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 11766 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 25, 'TRANS': 717} Chain breaks: 2 Chain: "C" Number of atoms: 8261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 8261 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain: "D" Number of atoms: 11715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 11715 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 25, 'TRANS': 714} Chain breaks: 2 Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 930 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 960 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Time building chain proxies: 7.33, per 1000 atoms: 0.17 Number of scatterers: 41912 At special positions: 0 Unit cell: (133.61, 143.954, 149.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 60 15.00 O 4157 8.00 N 3770 7.00 C 13134 6.00 H 20715 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4706 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 28 sheets defined 50.0% alpha, 14.4% beta 30 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.816A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.655A pdb=" N HIS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 136 No H-bonds generated for 'chain 'A' and resid 135 through 136' Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.940A pdb=" N GLU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 417 through 425 removed outlier: 4.150A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.784A pdb=" N HIS A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.602A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.897A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 removed outlier: 3.693A pdb=" N TYR B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.676A pdb=" N HIS B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.527A pdb=" N ALA B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.866A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 343 through 364 removed outlier: 4.517A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 386 removed outlier: 3.698A pdb=" N ALA B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.610A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.626A pdb=" N THR B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.644A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 576 through 597 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.767A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 removed outlier: 3.546A pdb=" N LEU B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 622' Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.728A pdb=" N THR B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 718 through 731 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 785 through 801 Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.692A pdb=" N HIS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.517A pdb=" N LEU C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.713A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.789A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.761A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.719A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.771A pdb=" N TYR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 removed outlier: 3.502A pdb=" N HIS D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.704A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 279 through 301 Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.552A pdb=" N LYS D 305 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 364 removed outlier: 3.897A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 386 removed outlier: 3.610A pdb=" N ILE D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.549A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.634A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.722A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 3.555A pdb=" N LEU D 620 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 622' Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.550A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.685A pdb=" N THR D 683 " --> pdb=" O HIS D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.773A pdb=" N MET D 755 " --> pdb=" O TRP D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 801 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.543A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 423 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 250 removed outlier: 4.566A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 444 removed outlier: 3.578A pdb=" N LEU A 447 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 139 through 145 removed outlier: 3.579A pdb=" N LYS B 129 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 168 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 169 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 69 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 60 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 59 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ARG B 206 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 61 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.529A pdb=" N PHE B 243 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 254 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 247 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.529A pdb=" N PHE B 243 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 254 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 322 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 321 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AB5, first strand: chain 'B' and resid 647 through 654 removed outlier: 3.796A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 8 through 12 removed outlier: 5.595A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 495 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 423 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 333 Processing sheet with id=AC2, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.575A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 303 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC4, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'D' and resid 139 through 145 removed outlier: 6.735A pdb=" N TRP D 170 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU D 130 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG D 168 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU D 132 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET D 166 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 69 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 60 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.761A pdb=" N LYS D 247 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.725A pdb=" N GLY D 251 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 265 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL D 323 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR D 267 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL D 325 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE D 269 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS D 268 " --> pdb=" O GLN D 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC9, first strand: chain 'D' and resid 565 through 567 Processing sheet with id=AD1, first strand: chain 'D' and resid 646 through 654 removed outlier: 3.536A pdb=" N LEU D 659 " --> pdb=" O ASN D 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 675 " --> pdb=" O VAL D 664 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3057 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 10.37 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 6927 1.05 - 1.24: 16468 1.24 - 1.43: 6319 1.43 - 1.62: 12534 1.62 - 1.81: 140 Bond restraints: 42388 Sorted by residual: bond pdb=" NE1 TRP C 436 " pdb=" HE1 TRP C 436 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP B 751 " pdb=" HE1 TRP B 751 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP B 258 " pdb=" HE1 TRP B 258 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP B 170 " pdb=" HE1 TRP B 170 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP D 258 " pdb=" HE1 TRP D 258 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 42383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.26: 76776 10.26 - 20.52: 5 20.52 - 30.79: 1 30.79 - 41.05: 0 41.05 - 51.31: 2 Bond angle restraints: 76784 Sorted by residual: angle pdb=" CA SER D 121 " pdb=" N SER D 121 " pdb=" H SER D 121 " ideal model delta sigma weight residual 114.00 165.31 -51.31 3.00e+00 1.11e-01 2.93e+02 angle pdb=" CA THR D 163 " pdb=" N THR D 163 " pdb=" H THR D 163 " ideal model delta sigma weight residual 114.00 156.34 -42.34 3.00e+00 1.11e-01 1.99e+02 angle pdb=" N VAL D 167 " pdb=" CA VAL D 167 " pdb=" C VAL D 167 " ideal model delta sigma weight residual 108.11 90.54 17.57 1.40e+00 5.10e-01 1.58e+02 angle pdb=" CA THR B 163 " pdb=" N THR B 163 " pdb=" H THR B 163 " ideal model delta sigma weight residual 114.00 143.64 -29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C VAL D 167 " pdb=" CA VAL D 167 " pdb=" CB VAL D 167 " ideal model delta sigma weight residual 110.63 121.91 -11.28 1.48e+00 4.57e-01 5.81e+01 ... (remaining 76779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 18945 33.79 - 67.57: 605 67.57 - 101.36: 2 101.36 - 135.14: 0 135.14 - 168.93: 2 Dihedral angle restraints: 19554 sinusoidal: 11308 harmonic: 8246 Sorted by residual: dihedral pdb=" CA GLY C 31 " pdb=" C GLY C 31 " pdb=" N ARG C 32 " pdb=" CA ARG C 32 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" C4' DT E 28 " pdb=" C3' DT E 28 " pdb=" O3' DT E 28 " pdb=" P DT E 29 " ideal model delta sinusoidal sigma weight residual 220.00 51.07 168.93 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA F 1 " pdb=" C3' DA F 1 " pdb=" O3' DA F 1 " pdb=" P DA F 2 " ideal model delta sinusoidal sigma weight residual 220.00 62.78 157.22 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 19551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2335 0.041 - 0.083: 673 0.083 - 0.124: 180 0.124 - 0.165: 103 0.165 - 0.207: 17 Chirality restraints: 3308 Sorted by residual: chirality pdb=" C3' DT E 20 " pdb=" C4' DT E 20 " pdb=" O3' DT E 20 " pdb=" C2' DT E 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' DA F 12 " pdb=" C4' DA F 12 " pdb=" O3' DA F 12 " pdb=" C2' DA F 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 3305 not shown) Planarity restraints: 6113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT E 6 " 0.014 2.00e-02 2.50e+03 1.38e-02 5.26e+00 pdb=" N1 DT E 6 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DT E 6 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT E 6 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT E 6 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT E 6 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DT E 6 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" H6 DT E 6 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 163 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 164 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 163 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 164 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.030 5.00e-02 4.00e+02 ... (remaining 6110 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.99: 314 1.99 - 2.64: 51860 2.64 - 3.29: 123738 3.29 - 3.95: 157769 3.95 - 4.60: 247733 Nonbonded interactions: 581414 Sorted by model distance: nonbonded pdb=" HG1 THR B 292 " pdb="HD23 LEU B 357 " model vdw 1.332 2.270 nonbonded pdb=" HG SER C 27 " pdb="HG21 VAL D 501 " model vdw 1.391 2.270 nonbonded pdb=" HG SER A 27 " pdb="HG21 VAL B 501 " model vdw 1.409 2.270 nonbonded pdb=" HG1 THR D 292 " pdb="HD23 LEU D 357 " model vdw 1.507 2.270 nonbonded pdb=" HZ2 LYS B 449 " pdb=" HD1 HIS B 505 " model vdw 1.538 2.100 ... (remaining 581409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 524) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 11 through 76 or resid 121 through 802)) selection = (chain 'D' and (resid 11 through 76 or resid 121 through 802)) } 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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 45.470 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.005 0.090 21673 Z= 0.283 Angle : 0.703 17.575 29528 Z= 0.450 Chirality : 0.048 0.207 3308 Planarity : 0.004 0.055 3659 Dihedral : 13.220 168.928 8464 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2508 helix: 1.83 (0.14), residues: 1156 sheet: -0.91 (0.26), residues: 406 loop : -1.16 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.012 0.001 TYR C 63 PHE 0.012 0.002 PHE B 196 TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.28 (21673) covalent geometry : angle 0.70323 / 0.45 (29528) hydrogen bonds : bond 0.16547 / 10.81 ( 1122) hydrogen bonds : angle 6.48553 / 4.68 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 513 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7983 (t0) cc_final: 0.7700 (m-30) REVERT: A 159 MET cc_start: 0.9373 (mmt) cc_final: 0.8944 (mmt) REVERT: A 231 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7364 (mp0) REVERT: A 487 GLU cc_start: 0.7793 (tp30) cc_final: 0.7418 (pt0) REVERT: A 508 LEU cc_start: 0.8744 (tp) cc_final: 0.8542 (tp) REVERT: B 21 LYS cc_start: 0.8542 (mttt) cc_final: 0.8167 (mmmt) REVERT: B 218 TYR cc_start: 0.7184 (m-80) cc_final: 0.6831 (m-80) REVERT: B 222 ILE cc_start: 0.7981 (mm) cc_final: 0.7748 (mp) REVERT: B 242 TYR cc_start: 0.8345 (t80) cc_final: 0.7831 (t80) REVERT: B 253 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 265 ASN cc_start: 0.7544 (m-40) cc_final: 0.7216 (m-40) REVERT: B 439 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7692 (mmtm) REVERT: B 474 LEU cc_start: 0.8223 (tp) cc_final: 0.7997 (tt) REVERT: B 569 ASN cc_start: 0.8054 (m110) cc_final: 0.7219 (m110) REVERT: B 640 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8307 (mtmt) REVERT: B 702 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6864 (mp0) REVERT: B 754 THR cc_start: 0.8229 (p) cc_final: 0.7078 (t) REVERT: C 141 GLU cc_start: 0.7899 (pt0) cc_final: 0.7301 (pp20) REVERT: C 371 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7466 (ttm110) REVERT: D 13 LEU cc_start: 0.7296 (mt) cc_final: 0.7035 (tp) REVERT: D 41 PHE cc_start: 0.7117 (m-10) cc_final: 0.6582 (m-10) REVERT: D 277 ASP cc_start: 0.7587 (m-30) cc_final: 0.7043 (t0) REVERT: D 359 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7271 (mm-30) REVERT: D 377 ASP cc_start: 0.7968 (t0) cc_final: 0.7574 (m-30) REVERT: D 439 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8081 (ttmp) REVERT: D 474 LEU cc_start: 0.7896 (tp) cc_final: 0.7602 (tp) REVERT: D 556 GLN cc_start: 0.7586 (mt0) cc_final: 0.7246 (mt0) REVERT: D 754 THR cc_start: 0.8417 (p) cc_final: 0.7573 (t) outliers start: 5 outliers final: 1 residues processed: 515 average time/residue: 1.6417 time to fit residues: 945.6472 Evaluate side-chains 258 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 106 GLN A 319 ASN A 464 GLN A 484 GLN B 46 ASN B 434 GLN B 531 GLN C 94 GLN C 327 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114971 restraints weight = 76608.782| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.88 r_work: 0.3242 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21673 Z= 0.159 Angle : 0.572 6.851 29528 Z= 0.320 Chirality : 0.043 0.206 3308 Planarity : 0.004 0.054 3659 Dihedral : 13.543 174.995 3496 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 13.18 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2508 helix: 2.34 (0.15), residues: 1179 sheet: -0.94 (0.26), residues: 387 loop : -1.06 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 206 TYR 0.009 0.001 TYR C 63 PHE 0.014 0.001 PHE B 262 TRP 0.004 0.001 TRP C 415 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (21673) covalent geometry : angle 0.57157 / 0.32 (29528) hydrogen bonds : bond 0.04951 / 3.17 ( 1122) hydrogen bonds : angle 5.15236 / 3.66 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: A 159 MET cc_start: 0.9257 (mmt) cc_final: 0.8666 (mmt) REVERT: A 231 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7651 (mp0) REVERT: A 416 GLN cc_start: 0.7617 (pp30) cc_final: 0.7412 (pp30) REVERT: A 487 GLU cc_start: 0.8017 (tp30) cc_final: 0.7519 (pt0) REVERT: B 21 LYS cc_start: 0.8604 (mttt) cc_final: 0.8238 (mmmt) REVERT: B 57 LYS cc_start: 0.8158 (tttm) cc_final: 0.7845 (tmtt) REVERT: B 169 PHE cc_start: 0.8067 (p90) cc_final: 0.7707 (p90) REVERT: B 218 TYR cc_start: 0.7210 (m-80) cc_final: 0.6858 (m-80) REVERT: B 242 TYR cc_start: 0.8432 (t80) cc_final: 0.8152 (t80) REVERT: B 253 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 265 ASN cc_start: 0.7956 (m-40) cc_final: 0.7725 (m-40) REVERT: B 346 LYS cc_start: 0.7975 (tttt) cc_final: 0.7750 (tttm) REVERT: B 439 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7909 (mmtm) REVERT: B 569 ASN cc_start: 0.8373 (m110) cc_final: 0.7412 (m110) REVERT: B 611 TYR cc_start: 0.8106 (m-80) cc_final: 0.7847 (m-80) REVERT: B 617 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7394 (tp30) REVERT: B 640 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8257 (mtmt) REVERT: B 702 GLU cc_start: 0.8091 (mm-30) cc_final: 0.6953 (mp0) REVERT: B 754 THR cc_start: 0.8214 (p) cc_final: 0.7414 (t) REVERT: B 793 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: C 141 GLU cc_start: 0.7946 (pt0) cc_final: 0.7341 (pp20) REVERT: C 371 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7752 (ttm110) REVERT: D 13 LEU cc_start: 0.7353 (mt) cc_final: 0.7057 (tp) REVERT: D 257 GLN cc_start: 0.7130 (tt0) cc_final: 0.6639 (tp-100) REVERT: D 277 ASP cc_start: 0.7661 (m-30) cc_final: 0.7244 (t0) REVERT: D 344 GLU cc_start: 0.6764 (pm20) cc_final: 0.6443 (pm20) REVERT: D 359 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7069 (mm-30) REVERT: D 377 ASP cc_start: 0.8050 (t0) cc_final: 0.7559 (m-30) REVERT: D 474 LEU cc_start: 0.7977 (tp) cc_final: 0.7723 (tp) REVERT: D 754 THR cc_start: 0.8286 (p) cc_final: 0.8064 (p) outliers start: 38 outliers final: 22 residues processed: 293 average time/residue: 1.4792 time to fit residues: 494.2645 Evaluate side-chains 251 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 73 optimal weight: 0.0040 chunk 201 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 464 GLN B 46 ASN B 542 GLN C 464 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111839 restraints weight = 76604.188| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.91 r_work: 0.3173 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21673 Z= 0.200 Angle : 0.554 6.521 29528 Z= 0.309 Chirality : 0.043 0.215 3308 Planarity : 0.004 0.065 3659 Dihedral : 13.565 171.093 3494 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.93 % Allowed : 14.45 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2508 helix: 2.31 (0.15), residues: 1186 sheet: -0.96 (0.26), residues: 390 loop : -1.15 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.011 0.001 TYR A 86 PHE 0.013 0.001 PHE B 285 TRP 0.013 0.001 TRP C 415 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (21673) covalent geometry : angle 0.55380 / 0.31 (29528) hydrogen bonds : bond 0.04667 / 2.96 ( 1122) hydrogen bonds : angle 4.85142 / 3.43 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8899 (ttm) cc_final: 0.8628 (ttp) REVERT: A 153 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: A 159 MET cc_start: 0.9268 (mmt) cc_final: 0.8696 (mmt) REVERT: A 231 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7660 (mp0) REVERT: A 306 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: A 416 GLN cc_start: 0.7865 (pp30) cc_final: 0.7638 (pp30) REVERT: B 21 LYS cc_start: 0.8610 (mttt) cc_final: 0.8246 (mmmt) REVERT: B 57 LYS cc_start: 0.8220 (tttm) cc_final: 0.7902 (tmtt) REVERT: B 169 PHE cc_start: 0.8118 (p90) cc_final: 0.7775 (p90) REVERT: B 218 TYR cc_start: 0.7172 (m-80) cc_final: 0.6884 (m-80) REVERT: B 242 TYR cc_start: 0.8456 (t80) cc_final: 0.8252 (t80) REVERT: B 253 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 265 ASN cc_start: 0.7967 (m-40) cc_final: 0.7745 (m-40) REVERT: B 294 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7214 (m110) REVERT: B 346 LYS cc_start: 0.8050 (tttt) cc_final: 0.7836 (tttm) REVERT: B 439 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7904 (mmtm) REVERT: B 569 ASN cc_start: 0.8354 (m110) cc_final: 0.7396 (m110) REVERT: B 617 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7331 (tp30) REVERT: B 640 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8190 (mtmt) REVERT: B 702 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7000 (mp0) REVERT: B 793 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: C 141 GLU cc_start: 0.8097 (pt0) cc_final: 0.7295 (pp20) REVERT: D 13 LEU cc_start: 0.7388 (mt) cc_final: 0.7096 (tp) REVERT: D 252 VAL cc_start: 0.8375 (t) cc_final: 0.8135 (p) REVERT: D 257 GLN cc_start: 0.7169 (tt0) cc_final: 0.6611 (tp-100) REVERT: D 277 ASP cc_start: 0.7652 (m-30) cc_final: 0.7268 (t0) REVERT: D 344 GLU cc_start: 0.6822 (pm20) cc_final: 0.6498 (pm20) REVERT: D 359 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7128 (mm-30) REVERT: D 377 ASP cc_start: 0.8065 (t0) cc_final: 0.7536 (m-30) REVERT: D 474 LEU cc_start: 0.8047 (tp) cc_final: 0.7789 (tp) REVERT: D 702 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: D 754 THR cc_start: 0.8516 (p) cc_final: 0.7929 (t) outliers start: 41 outliers final: 22 residues processed: 270 average time/residue: 1.4054 time to fit residues: 434.0484 Evaluate side-chains 247 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS B 46 ASN C 165 ASN D 55 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109637 restraints weight = 76571.045| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.02 r_work: 0.3135 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21673 Z= 0.250 Angle : 0.579 6.688 29528 Z= 0.323 Chirality : 0.044 0.216 3308 Planarity : 0.005 0.070 3659 Dihedral : 13.659 170.436 3494 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.26 % Allowed : 14.78 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2508 helix: 2.18 (0.15), residues: 1188 sheet: -1.01 (0.25), residues: 409 loop : -1.24 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.012 0.001 TYR A 86 PHE 0.011 0.002 PHE B 513 TRP 0.009 0.001 TRP C 415 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (21673) covalent geometry : angle 0.57917 / 0.32 (29528) hydrogen bonds : bond 0.04893 / 3.12 ( 1122) hydrogen bonds : angle 4.79165 / 3.38 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8894 (ttm) cc_final: 0.8649 (ttp) REVERT: A 153 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: A 159 MET cc_start: 0.9287 (mmt) cc_final: 0.8772 (mmt) REVERT: A 231 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7648 (mp0) REVERT: A 306 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 416 GLN cc_start: 0.7896 (pp30) cc_final: 0.7622 (pp30) REVERT: B 21 LYS cc_start: 0.8616 (mttt) cc_final: 0.8287 (mmmt) REVERT: B 57 LYS cc_start: 0.8248 (tttm) cc_final: 0.7930 (tmtt) REVERT: B 169 PHE cc_start: 0.8158 (p90) cc_final: 0.7825 (p90) REVERT: B 253 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 265 ASN cc_start: 0.7941 (m-40) cc_final: 0.7567 (m-40) REVERT: B 439 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7911 (mmtm) REVERT: B 465 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7731 (mp-120) REVERT: B 569 ASN cc_start: 0.8372 (m110) cc_final: 0.7361 (m110) REVERT: B 617 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7324 (tp30) REVERT: B 640 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8179 (mtmt) REVERT: B 702 GLU cc_start: 0.8174 (mm-30) cc_final: 0.6987 (mp0) REVERT: B 754 THR cc_start: 0.8370 (p) cc_final: 0.7970 (t) REVERT: B 793 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: C 106 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: C 141 GLU cc_start: 0.8208 (pt0) cc_final: 0.7243 (pp20) REVERT: D 13 LEU cc_start: 0.7407 (mt) cc_final: 0.7099 (tp) REVERT: D 131 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6621 (mp0) REVERT: D 252 VAL cc_start: 0.8355 (t) cc_final: 0.8141 (p) REVERT: D 257 GLN cc_start: 0.7170 (tt0) cc_final: 0.6587 (tp-100) REVERT: D 277 ASP cc_start: 0.7618 (m-30) cc_final: 0.7272 (t0) REVERT: D 344 GLU cc_start: 0.6843 (pm20) cc_final: 0.6514 (pm20) REVERT: D 377 ASP cc_start: 0.8113 (t0) cc_final: 0.7534 (m-30) REVERT: D 474 LEU cc_start: 0.8020 (tp) cc_final: 0.7755 (tp) REVERT: D 754 THR cc_start: 0.8645 (p) cc_final: 0.8039 (t) outliers start: 48 outliers final: 24 residues processed: 264 average time/residue: 1.3904 time to fit residues: 420.8102 Evaluate side-chains 243 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 720 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 146 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 202 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112432 restraints weight = 76166.626| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.98 r_work: 0.3178 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21673 Z= 0.116 Angle : 0.506 5.710 29528 Z= 0.283 Chirality : 0.041 0.217 3308 Planarity : 0.004 0.056 3659 Dihedral : 13.600 170.906 3494 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.60 % Allowed : 15.67 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2508 helix: 2.46 (0.15), residues: 1184 sheet: -1.03 (0.25), residues: 405 loop : -1.06 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 291 TYR 0.011 0.001 TYR D 228 PHE 0.024 0.001 PHE D 169 TRP 0.010 0.001 TRP C 415 HIS 0.004 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (21673) covalent geometry : angle 0.50639 / 0.28 (29528) hydrogen bonds : bond 0.03984 / 2.55 ( 1122) hydrogen bonds : angle 4.56091 / 3.22 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8851 (ttm) cc_final: 0.8591 (ttp) REVERT: A 153 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: A 159 MET cc_start: 0.9283 (mmt) cc_final: 0.8786 (mmt) REVERT: A 231 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7635 (mp0) REVERT: A 306 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 416 GLN cc_start: 0.7865 (pp30) cc_final: 0.7553 (pp30) REVERT: A 487 GLU cc_start: 0.8023 (tp30) cc_final: 0.7554 (pt0) REVERT: B 21 LYS cc_start: 0.8617 (mttt) cc_final: 0.8286 (mmmt) REVERT: B 57 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7894 (tmtt) REVERT: B 169 PHE cc_start: 0.8099 (p90) cc_final: 0.7791 (p90) REVERT: B 253 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 265 ASN cc_start: 0.7959 (m-40) cc_final: 0.7556 (m-40) REVERT: B 439 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7909 (mmtm) REVERT: B 562 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6354 (m-30) REVERT: B 569 ASN cc_start: 0.8308 (m110) cc_final: 0.7334 (m110) REVERT: B 617 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7304 (tp30) REVERT: B 640 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8142 (mtmt) REVERT: B 702 GLU cc_start: 0.8097 (mm-30) cc_final: 0.6731 (mp0) REVERT: B 754 THR cc_start: 0.8294 (p) cc_final: 0.7884 (t) REVERT: B 793 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: C 141 GLU cc_start: 0.8144 (pt0) cc_final: 0.7245 (pp20) REVERT: D 13 LEU cc_start: 0.7391 (mt) cc_final: 0.7079 (tp) REVERT: D 131 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6618 (mp0) REVERT: D 166 MET cc_start: 0.7271 (tmt) cc_final: 0.6849 (tmt) REVERT: D 252 VAL cc_start: 0.8342 (t) cc_final: 0.8135 (p) REVERT: D 277 ASP cc_start: 0.7622 (m-30) cc_final: 0.7286 (t0) REVERT: D 344 GLU cc_start: 0.6811 (pm20) cc_final: 0.6503 (pm20) REVERT: D 377 ASP cc_start: 0.8081 (t0) cc_final: 0.7533 (m-30) REVERT: D 474 LEU cc_start: 0.7996 (tp) cc_final: 0.7725 (tp) REVERT: D 702 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: D 754 THR cc_start: 0.8582 (p) cc_final: 0.8022 (t) outliers start: 34 outliers final: 19 residues processed: 248 average time/residue: 1.3869 time to fit residues: 394.6674 Evaluate side-chains 238 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 69 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 187 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115569 restraints weight = 76553.753| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.86 r_work: 0.3241 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 21673 Z= 0.110 Angle : 0.494 8.172 29528 Z= 0.277 Chirality : 0.041 0.305 3308 Planarity : 0.004 0.058 3659 Dihedral : 13.567 171.217 3494 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.51 % Allowed : 15.48 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2508 helix: 2.60 (0.15), residues: 1189 sheet: -0.89 (0.26), residues: 397 loop : -1.00 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.014 0.001 TYR D 228 PHE 0.077 0.001 PHE D 169 TRP 0.009 0.001 TRP C 415 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (21673) covalent geometry : angle 0.49406 / 0.28 (29528) hydrogen bonds : bond 0.03677 / 2.36 ( 1122) hydrogen bonds : angle 4.39062 / 3.10 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8813 (ttm) cc_final: 0.8550 (ttp) REVERT: A 153 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: A 159 MET cc_start: 0.9213 (mmt) cc_final: 0.8694 (mmt) REVERT: A 231 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7789 (mp0) REVERT: A 306 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: A 416 GLN cc_start: 0.7900 (pp30) cc_final: 0.7634 (pp30) REVERT: A 487 GLU cc_start: 0.7957 (tp30) cc_final: 0.7638 (pt0) REVERT: B 21 LYS cc_start: 0.8628 (mttt) cc_final: 0.8308 (mmmt) REVERT: B 57 LYS cc_start: 0.8258 (tttm) cc_final: 0.7943 (tmtt) REVERT: B 166 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.5928 (tmm) REVERT: B 169 PHE cc_start: 0.8140 (p90) cc_final: 0.7847 (p90) REVERT: B 253 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 265 ASN cc_start: 0.8062 (m-40) cc_final: 0.7707 (m-40) REVERT: B 426 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: B 562 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: B 569 ASN cc_start: 0.8343 (m110) cc_final: 0.7384 (m110) REVERT: B 640 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8163 (mtmt) REVERT: B 702 GLU cc_start: 0.8065 (mm-30) cc_final: 0.6754 (mp0) REVERT: B 754 THR cc_start: 0.8218 (p) cc_final: 0.7781 (t) REVERT: B 793 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: C 141 GLU cc_start: 0.7978 (pt0) cc_final: 0.7243 (pp20) REVERT: C 285 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7558 (mtp-110) REVERT: D 13 LEU cc_start: 0.7389 (mt) cc_final: 0.7100 (tp) REVERT: D 131 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6598 (mp0) REVERT: D 166 MET cc_start: 0.7258 (tmt) cc_final: 0.6875 (tmt) REVERT: D 204 ARG cc_start: 0.6971 (mtt-85) cc_final: 0.6503 (ttt180) REVERT: D 277 ASP cc_start: 0.7674 (m-30) cc_final: 0.7349 (t0) REVERT: D 344 GLU cc_start: 0.6769 (pm20) cc_final: 0.6497 (pm20) REVERT: D 377 ASP cc_start: 0.8123 (t0) cc_final: 0.7591 (m-30) REVERT: D 474 LEU cc_start: 0.7960 (tp) cc_final: 0.7719 (tp) REVERT: D 702 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: D 754 THR cc_start: 0.8485 (p) cc_final: 0.7937 (t) outliers start: 32 outliers final: 16 residues processed: 248 average time/residue: 1.4076 time to fit residues: 402.2892 Evaluate side-chains 237 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 132 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 255 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 243 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111314 restraints weight = 76297.716| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.88 r_work: 0.3193 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21673 Z= 0.205 Angle : 0.540 5.547 29528 Z= 0.300 Chirality : 0.042 0.213 3308 Planarity : 0.004 0.059 3659 Dihedral : 13.660 170.189 3494 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.65 % Allowed : 15.95 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2508 helix: 2.46 (0.15), residues: 1190 sheet: -1.00 (0.25), residues: 419 loop : -1.05 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 291 TYR 0.015 0.001 TYR D 228 PHE 0.041 0.002 PHE D 169 TRP 0.007 0.001 TRP C 415 HIS 0.006 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (21673) covalent geometry : angle 0.53969 / 0.30 (29528) hydrogen bonds : bond 0.04423 / 2.81 ( 1122) hydrogen bonds : angle 4.47849 / 3.16 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8861 (ttm) cc_final: 0.8608 (ttp) REVERT: A 153 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: A 159 MET cc_start: 0.9233 (mmt) cc_final: 0.8766 (mmt) REVERT: A 231 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7759 (mp0) REVERT: A 306 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: A 416 GLN cc_start: 0.7951 (pp30) cc_final: 0.7680 (pp30) REVERT: B 17 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 21 LYS cc_start: 0.8611 (mttt) cc_final: 0.8304 (mmmt) REVERT: B 57 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7943 (tmtt) REVERT: B 169 PHE cc_start: 0.8119 (p90) cc_final: 0.7823 (p90) REVERT: B 253 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 265 ASN cc_start: 0.8040 (m-40) cc_final: 0.7684 (m-40) REVERT: B 426 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: B 569 ASN cc_start: 0.8365 (m110) cc_final: 0.7450 (m110) REVERT: B 640 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8270 (mtpt) REVERT: B 702 GLU cc_start: 0.8098 (mm-30) cc_final: 0.6762 (mp0) REVERT: B 754 THR cc_start: 0.8345 (p) cc_final: 0.7957 (t) REVERT: B 793 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 141 GLU cc_start: 0.8135 (pt0) cc_final: 0.7254 (pp20) REVERT: D 13 LEU cc_start: 0.7400 (mt) cc_final: 0.7089 (tp) REVERT: D 131 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6563 (mp0) REVERT: D 277 ASP cc_start: 0.7705 (m-30) cc_final: 0.7395 (t0) REVERT: D 344 GLU cc_start: 0.6823 (pm20) cc_final: 0.6531 (pm20) REVERT: D 377 ASP cc_start: 0.8173 (t0) cc_final: 0.7572 (m-30) REVERT: D 474 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7737 (tp) REVERT: D 702 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6943 (mp0) outliers start: 35 outliers final: 21 residues processed: 236 average time/residue: 1.3166 time to fit residues: 356.2871 Evaluate side-chains 234 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 6 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112227 restraints weight = 76375.785| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.88 r_work: 0.3203 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21673 Z= 0.149 Angle : 0.512 6.059 29528 Z= 0.285 Chirality : 0.041 0.213 3308 Planarity : 0.004 0.050 3659 Dihedral : 13.653 170.420 3494 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.55 % Allowed : 16.24 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2508 helix: 2.49 (0.15), residues: 1190 sheet: -1.00 (0.26), residues: 385 loop : -1.02 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 276 TYR 0.023 0.001 TYR D 242 PHE 0.012 0.001 PHE D 196 TRP 0.009 0.001 TRP C 415 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (21673) covalent geometry : angle 0.51157 / 0.29 (29528) hydrogen bonds : bond 0.04062 / 2.59 ( 1122) hydrogen bonds : angle 4.41235 / 3.12 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8852 (ttm) cc_final: 0.8595 (ttp) REVERT: A 153 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: A 159 MET cc_start: 0.9235 (mmt) cc_final: 0.8769 (mmt) REVERT: A 231 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7753 (mp0) REVERT: A 306 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: A 416 GLN cc_start: 0.7945 (pp30) cc_final: 0.7693 (pp30) REVERT: A 487 GLU cc_start: 0.7948 (tp30) cc_final: 0.7609 (pt0) REVERT: B 21 LYS cc_start: 0.8615 (mttt) cc_final: 0.8305 (mmmt) REVERT: B 57 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: B 169 PHE cc_start: 0.8098 (p90) cc_final: 0.7859 (p90) REVERT: B 253 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 265 ASN cc_start: 0.8041 (m-40) cc_final: 0.7669 (m-40) REVERT: B 426 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: B 569 ASN cc_start: 0.8320 (m110) cc_final: 0.7384 (m110) REVERT: B 640 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8249 (mtpt) REVERT: B 702 GLU cc_start: 0.8066 (mm-30) cc_final: 0.6724 (mp0) REVERT: B 754 THR cc_start: 0.8343 (p) cc_final: 0.7950 (t) REVERT: B 793 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: C 141 GLU cc_start: 0.8111 (pt0) cc_final: 0.7237 (pp20) REVERT: D 13 LEU cc_start: 0.7410 (mt) cc_final: 0.7079 (tp) REVERT: D 131 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6398 (mp0) REVERT: D 277 ASP cc_start: 0.7690 (m-30) cc_final: 0.7390 (t0) REVERT: D 344 GLU cc_start: 0.6810 (pm20) cc_final: 0.6510 (pm20) REVERT: D 377 ASP cc_start: 0.8148 (t0) cc_final: 0.7565 (m-30) REVERT: D 474 LEU cc_start: 0.7967 (tp) cc_final: 0.7714 (tp) REVERT: D 702 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: D 754 THR cc_start: 0.8575 (p) cc_final: 0.8063 (t) outliers start: 33 outliers final: 21 residues processed: 238 average time/residue: 1.2931 time to fit residues: 354.9427 Evaluate side-chains 236 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 151 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112083 restraints weight = 76555.133| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.88 r_work: 0.3209 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21673 Z= 0.152 Angle : 0.512 7.588 29528 Z= 0.284 Chirality : 0.041 0.212 3308 Planarity : 0.004 0.054 3659 Dihedral : 13.681 170.615 3494 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.74 % Allowed : 16.19 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2508 helix: 2.50 (0.15), residues: 1190 sheet: -1.05 (0.26), residues: 390 loop : -0.98 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 291 TYR 0.016 0.001 TYR D 228 PHE 0.013 0.001 PHE D 196 TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (21673) covalent geometry : angle 0.51153 / 0.28 (29528) hydrogen bonds : bond 0.04007 / 2.56 ( 1122) hydrogen bonds : angle 4.37198 / 3.09 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8849 (ttm) cc_final: 0.8591 (ttp) REVERT: A 153 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: A 159 MET cc_start: 0.9234 (mmt) cc_final: 0.8777 (mmt) REVERT: A 231 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7752 (mp0) REVERT: A 306 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 416 GLN cc_start: 0.7946 (pp30) cc_final: 0.7700 (pp30) REVERT: A 487 GLU cc_start: 0.7949 (tp30) cc_final: 0.7613 (pt0) REVERT: B 17 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: B 21 LYS cc_start: 0.8592 (mttt) cc_final: 0.8296 (mmmt) REVERT: B 57 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7984 (tmtt) REVERT: B 169 PHE cc_start: 0.8198 (p90) cc_final: 0.7902 (p90) REVERT: B 253 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 265 ASN cc_start: 0.8040 (m-40) cc_final: 0.7673 (m-40) REVERT: B 426 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: B 569 ASN cc_start: 0.8311 (m110) cc_final: 0.7433 (m110) REVERT: B 640 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8234 (mtpt) REVERT: B 702 GLU cc_start: 0.8059 (mm-30) cc_final: 0.6737 (mp0) REVERT: B 754 THR cc_start: 0.8333 (p) cc_final: 0.7939 (t) REVERT: B 793 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: C 141 GLU cc_start: 0.8102 (pt0) cc_final: 0.7231 (pp20) REVERT: D 13 LEU cc_start: 0.7409 (mt) cc_final: 0.7078 (tp) REVERT: D 131 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6652 (mp0) REVERT: D 277 ASP cc_start: 0.7695 (m-30) cc_final: 0.7416 (t0) REVERT: D 344 GLU cc_start: 0.6785 (pm20) cc_final: 0.6482 (pm20) REVERT: D 377 ASP cc_start: 0.8153 (t0) cc_final: 0.7581 (m-30) REVERT: D 474 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7727 (tp) REVERT: D 653 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8052 (t) REVERT: D 702 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: D 754 THR cc_start: 0.8556 (p) cc_final: 0.8066 (t) outliers start: 37 outliers final: 21 residues processed: 243 average time/residue: 1.2707 time to fit residues: 357.7164 Evaluate side-chains 239 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 230 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112987 restraints weight = 76366.368| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.85 r_work: 0.3215 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21673 Z= 0.133 Angle : 0.502 6.664 29528 Z= 0.279 Chirality : 0.040 0.212 3308 Planarity : 0.004 0.050 3659 Dihedral : 13.684 170.626 3494 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.46 % Allowed : 16.56 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2508 helix: 2.54 (0.15), residues: 1189 sheet: -1.01 (0.25), residues: 398 loop : -0.91 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 291 TYR 0.016 0.001 TYR D 228 PHE 0.031 0.001 PHE D 169 TRP 0.010 0.001 TRP C 415 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21673) covalent geometry : angle 0.50202 / 0.28 (29528) hydrogen bonds : bond 0.03871 / 2.47 ( 1122) hydrogen bonds : angle 4.32363 / 3.06 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8835 (ttm) cc_final: 0.8573 (ttp) REVERT: A 153 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: A 159 MET cc_start: 0.9235 (mmt) cc_final: 0.8780 (mmt) REVERT: A 231 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7746 (mp0) REVERT: A 306 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: A 416 GLN cc_start: 0.7924 (pp30) cc_final: 0.7681 (pp30) REVERT: A 487 GLU cc_start: 0.7934 (tp30) cc_final: 0.7604 (pt0) REVERT: B 17 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: B 21 LYS cc_start: 0.8587 (mttt) cc_final: 0.8299 (mmmt) REVERT: B 57 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7974 (tmtt) REVERT: B 166 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.5914 (tmm) REVERT: B 169 PHE cc_start: 0.8171 (p90) cc_final: 0.7875 (p90) REVERT: B 253 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 265 ASN cc_start: 0.8054 (m-40) cc_final: 0.7688 (m-40) REVERT: B 426 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: B 640 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8225 (mtpt) REVERT: B 702 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 754 THR cc_start: 0.8327 (p) cc_final: 0.7924 (t) REVERT: B 793 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 141 GLU cc_start: 0.8096 (pt0) cc_final: 0.7239 (pp20) REVERT: D 13 LEU cc_start: 0.7406 (mt) cc_final: 0.7073 (tp) REVERT: D 131 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6640 (mp0) REVERT: D 277 ASP cc_start: 0.7721 (m-30) cc_final: 0.7445 (t0) REVERT: D 344 GLU cc_start: 0.6814 (pm20) cc_final: 0.6518 (pm20) REVERT: D 377 ASP cc_start: 0.8159 (t0) cc_final: 0.7594 (m-30) REVERT: D 474 LEU cc_start: 0.7969 (tp) cc_final: 0.7721 (tp) REVERT: D 653 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7959 (t) REVERT: D 702 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: D 754 THR cc_start: 0.8509 (p) cc_final: 0.8018 (t) outliers start: 31 outliers final: 20 residues processed: 233 average time/residue: 1.2847 time to fit residues: 344.9793 Evaluate side-chains 235 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 213 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114002 restraints weight = 76733.275| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.83 r_work: 0.3241 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21673 Z= 0.108 Angle : 0.489 6.900 29528 Z= 0.271 Chirality : 0.040 0.211 3308 Planarity : 0.003 0.051 3659 Dihedral : 13.658 170.855 3494 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.32 % Allowed : 16.75 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2508 helix: 2.66 (0.15), residues: 1183 sheet: -0.94 (0.26), residues: 399 loop : -0.84 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 291 TYR 0.023 0.001 TYR D 242 PHE 0.013 0.001 PHE D 196 TRP 0.009 0.001 TRP C 415 HIS 0.005 0.000 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (21673) covalent geometry : angle 0.48885 / 0.27 (29528) hydrogen bonds : bond 0.03585 / 2.29 ( 1122) hydrogen bonds : angle 4.23255 / 3.00 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14233.75 seconds wall clock time: 241 minutes 10.94 seconds (14470.94 seconds total)