Starting phenix.real_space_refine on Mon Aug 10 03:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqs_18603/08_2026/8qqs_18603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqs_18603/08_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_18603/08_2026/8qqs_18603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2026/8qqs_18603.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2026/8qqs_18603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 6.88, per 1000 atoms: 0.16 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: 4.29 Conformation dependent library (CDL) restraints added in 1.5 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: 7.97 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: 11.18 Time building geometry restraints manager: 6.05 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 48.330 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.880 ------------------------------------------------------------------------------- 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 : 0.704 17.575 29528 Z= 0.451 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 0.70426 / 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 : 1.130 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: 0.7701 (m-30) REVERT: A 159 MET cc_start: 0.9373 (mmt) cc_final: 0.8945 (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: 0.7749 (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: 0.7332 (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: 0.7693 (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: 0.7079 (t) REVERT: C 141 GLU cc_start: 0.7899 (pt0) cc_final: 0.7302 (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: 0.7270 (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: 0.7247 (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: 1.5644 time to fit residues: 903.9606 Evaluate side-chains 257 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.153303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114861 restraints weight = 76596.879| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.90 r_work: 0.3237 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21673 Z= 0.162 Angle : 0.565 6.983 29528 Z= 0.319 Chirality : 0.043 0.214 3308 Planarity : 0.004 0.055 3659 Dihedral : 13.539 173.998 3496 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.69 % Allowed : 13.36 % Favored : 84.94 % 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: 0.88 (0.17), residues: 2508 helix: 2.35 (0.15), residues: 1179 sheet: -0.95 (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 149 PHE 0.015 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 0.56535 / 0.32 (29528) hydrogen bonds : bond 0.04982 / 3.19 ( 1122) hydrogen bonds : angle 5.14027 / 3.65 ( 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 302 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.001 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: 0.8668 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: A 159 MET cc_start: 0.9259 (mmt) cc_final: 0.8670 (mmt) REVERT: A 231 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7653 (mp0) REVERT: A 416 GLN cc_start: 0.7623 (pp30) cc_final: 0.7413 (pp30) REVERT: A 487 GLU cc_start: 0.8034 (tp30) cc_final: 0.7511 (pt0) REVERT: B 21 LYS cc_start: 0.8603 (mttt) cc_final: 0.8235 (mmmt) REVERT: B 57 LYS cc_start: 0.8147 (tttm) cc_final: 0.7830 (tmtt) REVERT: B 169 PHE cc_start: 0.8055 (p90) cc_final: 0.7692 (p90) REVERT: B 218 TYR cc_start: 0.7197 (m-80) cc_final: 0.6849 (m-80) REVERT: B 242 TYR cc_start: 0.8417 (t80) cc_final: 0.8160 (t80) REVERT: B 253 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 265 ASN cc_start: 0.7964 (m-40) cc_final: 0.7735 (m-40) REVERT: B 346 LYS cc_start: 0.7968 (tttt) cc_final: 0.7742 (tttm) REVERT: B 439 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7906 (mmtm) REVERT: B 569 ASN cc_start: 0.8374 (m110) cc_final: 0.7440 (m110) REVERT: B 611 TYR cc_start: 0.8106 (m-80) cc_final: 0.7849 (m-80) REVERT: B 617 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7390 (tp30) REVERT: B 640 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8251 (mtmt) REVERT: B 702 GLU cc_start: 0.8093 (mm-30) cc_final: 0.6969 (mp0) REVERT: B 754 THR cc_start: 0.8223 (p) cc_final: 0.7420 (t) REVERT: B 793 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: C 141 GLU cc_start: 0.7949 (pt0) cc_final: 0.7347 (pp20) REVERT: C 371 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7743 (ttm110) REVERT: D 13 LEU cc_start: 0.7351 (mt) cc_final: 0.7052 (tp) REVERT: D 257 GLN cc_start: 0.7126 (tt0) cc_final: 0.6630 (tp-100) REVERT: D 277 ASP cc_start: 0.7661 (m-30) cc_final: 0.7240 (t0) REVERT: D 344 GLU cc_start: 0.6779 (pm20) cc_final: 0.6452 (pm20) REVERT: D 359 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7074 (mm-30) REVERT: D 377 ASP cc_start: 0.8048 (t0) cc_final: 0.7554 (m-30) REVERT: D 474 LEU cc_start: 0.7981 (tp) cc_final: 0.7726 (tp) REVERT: D 754 THR cc_start: 0.8304 (p) cc_final: 0.8083 (p) outliers start: 36 outliers final: 21 residues processed: 291 average time/residue: 1.3186 time to fit residues: 437.7356 Evaluate side-chains 250 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 250 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.151551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113186 restraints weight = 76549.685| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.90 r_work: 0.3198 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21673 Z= 0.149 Angle : 0.529 6.635 29528 Z= 0.294 Chirality : 0.042 0.235 3308 Planarity : 0.004 0.072 3659 Dihedral : 13.507 169.882 3494 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 14.45 % Favored : 83.86 % 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: 0.91 (0.17), residues: 2508 helix: 2.40 (0.15), residues: 1187 sheet: -0.96 (0.26), residues: 390 loop : -1.09 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 276 TYR 0.009 0.001 TYR A 86 PHE 0.014 0.001 PHE B 285 TRP 0.015 0.001 TRP C 415 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (21673) covalent geometry : angle 0.52906 / 0.29 (29528) hydrogen bonds : bond 0.04342 / 2.76 ( 1122) hydrogen bonds : angle 4.75103 / 3.36 ( 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 279 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.889 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: 0.8874 (ttm) cc_final: 0.8590 (ttp) REVERT: A 153 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: A 159 MET cc_start: 0.9263 (mmt) cc_final: 0.8659 (mmt) REVERT: A 231 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7590 (mp0) REVERT: A 306 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 416 GLN cc_start: 0.7806 (pp30) cc_final: 0.7572 (pp30) REVERT: B 21 LYS cc_start: 0.8579 (mttt) cc_final: 0.8233 (mmmt) REVERT: B 57 LYS cc_start: 0.8220 (tttm) cc_final: 0.7906 (tmtt) REVERT: B 169 PHE cc_start: 0.8099 (p90) cc_final: 0.7750 (p90) REVERT: B 218 TYR cc_start: 0.7140 (m-80) cc_final: 0.6775 (m-80) REVERT: B 253 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 265 ASN cc_start: 0.7953 (m-40) cc_final: 0.7725 (m-40) REVERT: B 294 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7215 (m110) REVERT: B 346 LYS cc_start: 0.7979 (tttt) cc_final: 0.7764 (tttm) REVERT: B 439 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7866 (mmtm) REVERT: B 569 ASN cc_start: 0.8293 (m110) cc_final: 0.7371 (m110) REVERT: B 617 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7355 (tp30) REVERT: B 640 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8140 (mtmt) REVERT: B 702 GLU cc_start: 0.8125 (mm-30) cc_final: 0.6974 (mp0) REVERT: B 793 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: C 141 GLU cc_start: 0.8052 (pt0) cc_final: 0.7261 (pp20) REVERT: D 13 LEU cc_start: 0.7381 (mt) cc_final: 0.7089 (tp) REVERT: D 252 VAL cc_start: 0.8343 (t) cc_final: 0.8111 (p) REVERT: D 257 GLN cc_start: 0.7148 (tt0) cc_final: 0.6613 (tp-100) REVERT: D 277 ASP cc_start: 0.7592 (m-30) cc_final: 0.7226 (t0) REVERT: D 344 GLU cc_start: 0.6790 (pm20) cc_final: 0.6505 (pm20) REVERT: D 350 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: D 359 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7126 (mm-30) REVERT: D 377 ASP cc_start: 0.8039 (t0) cc_final: 0.7509 (m-30) REVERT: D 474 LEU cc_start: 0.8012 (tp) cc_final: 0.7753 (tp) REVERT: D 702 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 754 THR cc_start: 0.8467 (p) cc_final: 0.7896 (t) outliers start: 36 outliers final: 18 residues processed: 263 average time/residue: 1.2687 time to fit residues: 383.3736 Evaluate side-chains 245 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 344 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 17 ASP 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 585 SER Chi-restraints excluded: chain B residue 661 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 350 GLU 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: 5.9990 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS B 46 ASN D 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110279 restraints weight = 76635.279| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.01 r_work: 0.3145 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21673 Z= 0.231 Angle : 0.563 6.483 29528 Z= 0.314 Chirality : 0.043 0.223 3308 Planarity : 0.004 0.067 3659 Dihedral : 13.615 170.309 3494 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.16 % Allowed : 14.59 % Favored : 83.25 % 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: 1188 sheet: -0.98 (0.25), residues: 409 loop : -1.15 (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 B 242 PHE 0.011 0.002 PHE B 513 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 0.00535 / 0.23 (21673) covalent geometry : angle 0.56252 / 0.31 (29528) hydrogen bonds : bond 0.04705 / 3.00 ( 1122) hydrogen bonds : angle 4.69728 / 3.31 ( 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 279 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.883 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: 0.8887 (ttm) cc_final: 0.8612 (ttp) REVERT: A 153 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 159 MET cc_start: 0.9284 (mmt) cc_final: 0.8748 (mmt) REVERT: A 231 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7619 (mp0) REVERT: A 416 GLN cc_start: 0.7871 (pp30) cc_final: 0.7567 (pp30) REVERT: B 21 LYS cc_start: 0.8616 (mttt) cc_final: 0.8280 (mmmt) REVERT: B 57 LYS cc_start: 0.8204 (tttm) cc_final: 0.7881 (tmtt) REVERT: B 169 PHE cc_start: 0.8097 (p90) cc_final: 0.7733 (p90) REVERT: B 253 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 265 ASN cc_start: 0.7953 (m-40) cc_final: 0.7566 (m-40) REVERT: B 439 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7903 (mmtm) REVERT: B 569 ASN cc_start: 0.8314 (m110) cc_final: 0.7377 (m110) REVERT: B 617 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7305 (tp30) REVERT: B 640 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8175 (mtmt) REVERT: B 702 GLU cc_start: 0.8134 (mm-30) cc_final: 0.6888 (mp0) REVERT: B 754 THR cc_start: 0.8362 (p) cc_final: 0.7927 (t) REVERT: B 793 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: C 141 GLU cc_start: 0.8166 (pt0) cc_final: 0.7223 (pp20) REVERT: C 285 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7514 (mtp-110) REVERT: D 13 LEU cc_start: 0.7394 (mt) cc_final: 0.7081 (tp) REVERT: D 131 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6539 (mp0) REVERT: D 204 ARG cc_start: 0.7069 (mtt-85) cc_final: 0.6690 (tpp-160) REVERT: D 252 VAL cc_start: 0.8347 (t) cc_final: 0.8129 (p) REVERT: D 257 GLN cc_start: 0.7168 (tt0) cc_final: 0.6599 (tp-100) REVERT: D 277 ASP cc_start: 0.7642 (m-30) cc_final: 0.7298 (t0) REVERT: D 344 GLU cc_start: 0.6845 (pm20) cc_final: 0.6520 (pm20) REVERT: D 377 ASP cc_start: 0.8067 (t0) cc_final: 0.7498 (m-30) REVERT: D 474 LEU cc_start: 0.8012 (tp) cc_final: 0.7742 (tp) REVERT: D 754 THR cc_start: 0.8624 (p) cc_final: 0.8026 (t) outliers start: 46 outliers final: 28 residues processed: 266 average time/residue: 1.2470 time to fit residues: 380.5549 Evaluate side-chains 245 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 464 GLN 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 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 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 585 SER 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 65 LYS 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 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: 0.9980 chunk 150 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 GLN C 57 ASN C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110769 restraints weight = 76284.899| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.03 r_work: 0.3146 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21673 Z= 0.174 Angle : 0.531 5.663 29528 Z= 0.296 Chirality : 0.042 0.235 3308 Planarity : 0.004 0.057 3659 Dihedral : 13.631 169.922 3494 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.88 % Allowed : 15.39 % 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: 0.84 (0.17), residues: 2508 helix: 2.34 (0.15), residues: 1190 sheet: -0.95 (0.25), residues: 412 loop : -1.14 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.012 0.001 TYR D 228 PHE 0.011 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 0.00398 / 0.17 (21673) covalent geometry : angle 0.53081 / 0.30 (29528) hydrogen bonds : bond 0.04333 / 2.76 ( 1122) hydrogen bonds : angle 4.59974 / 3.24 ( 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 261 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.066 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: 0.8875 (ttm) cc_final: 0.8622 (ttp) REVERT: A 153 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: A 159 MET cc_start: 0.9278 (mmt) cc_final: 0.8771 (mmt) REVERT: A 231 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7640 (mp0) REVERT: A 306 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 416 GLN cc_start: 0.7907 (pp30) cc_final: 0.7614 (pp30) REVERT: B 21 LYS cc_start: 0.8619 (mttt) cc_final: 0.8293 (mmmt) REVERT: B 57 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7902 (tmtt) REVERT: B 169 PHE cc_start: 0.8114 (p90) cc_final: 0.7791 (p90) REVERT: B 253 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 265 ASN cc_start: 0.7968 (m-40) cc_final: 0.7574 (m-40) REVERT: B 294 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.7120 (m110) REVERT: B 439 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7915 (mmtm) REVERT: B 465 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7755 (mp-120) REVERT: B 569 ASN cc_start: 0.8316 (m110) cc_final: 0.7354 (m110) REVERT: B 617 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7295 (tp30) REVERT: B 640 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8170 (mtmt) REVERT: B 702 GLU cc_start: 0.8113 (mm-30) cc_final: 0.6736 (mp0) REVERT: B 754 THR cc_start: 0.8322 (p) cc_final: 0.7932 (t) REVERT: B 793 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: C 106 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: C 141 GLU cc_start: 0.8194 (pt0) cc_final: 0.7249 (pp20) REVERT: D 13 LEU cc_start: 0.7400 (mt) cc_final: 0.7093 (tp) REVERT: D 131 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6560 (mp0) REVERT: D 166 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6198 (tmm) REVERT: D 204 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.6758 (tpp-160) REVERT: D 252 VAL cc_start: 0.8349 (t) cc_final: 0.8148 (p) REVERT: D 277 ASP cc_start: 0.7628 (m-30) cc_final: 0.7296 (t0) REVERT: D 344 GLU cc_start: 0.6827 (pm20) cc_final: 0.6519 (pm20) REVERT: D 377 ASP cc_start: 0.8138 (t0) cc_final: 0.7553 (m-30) REVERT: D 474 LEU cc_start: 0.8014 (tp) cc_final: 0.7745 (tp) REVERT: D 624 GLN cc_start: 0.7935 (mm110) cc_final: 0.7732 (mt0) REVERT: D 702 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: D 704 ASP cc_start: 0.7085 (t0) cc_final: 0.6858 (t0) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 1.2761 time to fit residues: 363.2280 Evaluate side-chains 239 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 57 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 465 GLN 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 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 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 69 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 453 GLN A 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110209 restraints weight = 76476.141| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.97 r_work: 0.3148 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21673 Z= 0.179 Angle : 0.526 5.669 29528 Z= 0.293 Chirality : 0.041 0.230 3308 Planarity : 0.004 0.046 3659 Dihedral : 13.654 170.199 3494 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.02 % Allowed : 15.39 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.17), residues: 2508 helix: 2.33 (0.15), residues: 1190 sheet: -1.05 (0.25), residues: 407 loop : -1.10 (0.19), residues: 911 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 0.010 0.001 PHE D 196 TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (21673) covalent geometry : angle 0.52642 / 0.29 (29528) hydrogen bonds : bond 0.04314 / 2.75 ( 1122) hydrogen bonds : angle 4.55804 / 3.21 ( 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 256 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.147 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: 0.8863 (ttm) cc_final: 0.8609 (ttp) REVERT: A 153 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: A 159 MET cc_start: 0.9281 (mmt) cc_final: 0.8830 (mmt) REVERT: A 231 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7630 (mp0) REVERT: A 306 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: A 416 GLN cc_start: 0.7906 (pp30) cc_final: 0.7619 (pp30) REVERT: B 21 LYS cc_start: 0.8616 (mttt) cc_final: 0.8296 (mmmt) REVERT: B 57 LYS cc_start: 0.8257 (tttm) cc_final: 0.7926 (tmtt) REVERT: B 166 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.5798 (tmm) REVERT: B 169 PHE cc_start: 0.8125 (p90) cc_final: 0.7807 (p90) REVERT: B 253 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 265 ASN cc_start: 0.7979 (m-40) cc_final: 0.7590 (m-40) REVERT: B 439 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7903 (mmtm) REVERT: B 465 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7747 (mp-120) REVERT: B 569 ASN cc_start: 0.8336 (m110) cc_final: 0.7373 (m110) REVERT: B 617 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7284 (tp30) REVERT: B 640 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8141 (mtmt) REVERT: B 702 GLU cc_start: 0.8114 (mm-30) cc_final: 0.6740 (mp0) REVERT: B 754 THR cc_start: 0.8352 (p) cc_final: 0.7971 (t) REVERT: B 793 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: C 106 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: C 141 GLU cc_start: 0.8203 (pt0) cc_final: 0.7241 (pp20) REVERT: C 285 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7637 (mtp-110) REVERT: D 13 LEU cc_start: 0.7390 (mt) cc_final: 0.7075 (tp) REVERT: D 131 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6520 (mp0) REVERT: D 166 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: D 204 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6757 (tpp-160) REVERT: D 277 ASP cc_start: 0.7635 (m-30) cc_final: 0.7325 (t0) REVERT: D 344 GLU cc_start: 0.6846 (pm20) cc_final: 0.6529 (pm20) REVERT: D 377 ASP cc_start: 0.8135 (t0) cc_final: 0.7515 (m-30) REVERT: D 474 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7713 (tp) REVERT: D 624 GLN cc_start: 0.7944 (mm110) cc_final: 0.7732 (mt0) REVERT: D 702 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: D 754 THR cc_start: 0.8659 (p) cc_final: 0.8074 (t) outliers start: 43 outliers final: 25 residues processed: 241 average time/residue: 1.1730 time to fit residues: 325.4291 Evaluate side-chains 243 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 130 ILE 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 17 ASP 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 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 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 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 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 166 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 255 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 243 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.148876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109833 restraints weight = 76273.662| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.93 r_work: 0.3147 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21673 Z= 0.169 Angle : 0.522 5.509 29528 Z= 0.292 Chirality : 0.041 0.230 3308 Planarity : 0.004 0.048 3659 Dihedral : 13.670 170.182 3494 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 15.34 % Favored : 82.49 % 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: 0.90 (0.17), residues: 2508 helix: 2.40 (0.15), residues: 1184 sheet: -1.03 (0.25), residues: 407 loop : -1.07 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 291 TYR 0.013 0.001 TYR D 228 PHE 0.023 0.001 PHE D 169 TRP 0.008 0.001 TRP C 415 HIS 0.004 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (21673) covalent geometry : angle 0.52201 / 0.29 (29528) hydrogen bonds : bond 0.04238 / 2.70 ( 1122) hydrogen bonds : angle 4.50802 / 3.18 ( 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 257 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.123 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: 0.8870 (ttm) cc_final: 0.8615 (ttp) REVERT: A 153 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: A 159 MET cc_start: 0.9288 (mmt) cc_final: 0.8841 (mmt) REVERT: A 231 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7609 (mp0) REVERT: A 306 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 416 GLN cc_start: 0.7884 (pp30) cc_final: 0.7594 (pp30) REVERT: B 21 LYS cc_start: 0.8609 (mttt) cc_final: 0.8295 (mmmt) REVERT: B 57 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7952 (tmtt) REVERT: B 166 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.5783 (tmm) REVERT: B 169 PHE cc_start: 0.8086 (p90) cc_final: 0.7761 (p90) REVERT: B 253 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 294 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7094 (m110) REVERT: B 439 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7904 (mmtm) REVERT: B 569 ASN cc_start: 0.8330 (m110) cc_final: 0.7357 (m110) REVERT: B 640 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8124 (mtmt) REVERT: B 702 GLU cc_start: 0.8104 (mm-30) cc_final: 0.6726 (mp0) REVERT: B 754 THR cc_start: 0.8377 (p) cc_final: 0.8003 (t) REVERT: B 793 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: C 106 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: C 141 GLU cc_start: 0.8209 (pt0) cc_final: 0.7227 (pp20) REVERT: D 13 LEU cc_start: 0.7404 (mt) cc_final: 0.7060 (tp) REVERT: D 131 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6401 (mp0) REVERT: D 166 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6367 (tmt) REVERT: D 204 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.6773 (tpp-160) REVERT: D 277 ASP cc_start: 0.7634 (m-30) cc_final: 0.7319 (t0) REVERT: D 344 GLU cc_start: 0.6774 (pm20) cc_final: 0.6457 (pm20) REVERT: D 377 ASP cc_start: 0.8121 (t0) cc_final: 0.7513 (m-30) REVERT: D 474 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7692 (tp) REVERT: D 624 GLN cc_start: 0.7970 (mm110) cc_final: 0.7745 (mt0) REVERT: D 702 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: D 754 THR cc_start: 0.8637 (p) cc_final: 0.8171 (t) outliers start: 46 outliers final: 30 residues processed: 242 average time/residue: 1.2428 time to fit residues: 346.7718 Evaluate side-chains 246 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE 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 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 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 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 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 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 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 166 MET Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 720 GLU Chi-restraints excluded: chain D residue 730 SER 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: 9.9990 chunk 161 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.149410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110772 restraints weight = 76296.346| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.93 r_work: 0.3156 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21673 Z= 0.150 Angle : 0.517 8.094 29528 Z= 0.290 Chirality : 0.041 0.270 3308 Planarity : 0.004 0.061 3659 Dihedral : 13.673 170.318 3494 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.31 % Allowed : 15.39 % Favored : 82.31 % 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: 0.98 (0.17), residues: 2508 helix: 2.48 (0.15), residues: 1183 sheet: -1.03 (0.26), residues: 385 loop : -1.00 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.014 0.001 TYR D 228 PHE 0.115 0.002 PHE D 169 TRP 0.014 0.001 TRP D 170 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (21673) covalent geometry : angle 0.51716 / 0.29 (29528) hydrogen bonds : bond 0.04088 / 2.62 ( 1122) hydrogen bonds : angle 4.45702 / 3.15 ( 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 268 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.844 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: 0.8680 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: A 159 MET cc_start: 0.9293 (mmt) cc_final: 0.8844 (mmt) REVERT: A 231 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7592 (mp0) REVERT: A 306 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 416 GLN cc_start: 0.7856 (pp30) cc_final: 0.7576 (pp30) REVERT: A 487 GLU cc_start: 0.8013 (tp30) cc_final: 0.7524 (pt0) REVERT: B 17 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: B 21 LYS cc_start: 0.8611 (mttt) cc_final: 0.8301 (mmmt) REVERT: B 57 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7963 (tmtt) REVERT: B 166 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.5754 (tmm) REVERT: B 169 PHE cc_start: 0.8059 (p90) cc_final: 0.7795 (p90) REVERT: B 253 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 294 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7099 (m110) REVERT: B 439 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7892 (mmtm) REVERT: B 569 ASN cc_start: 0.8288 (m110) cc_final: 0.7337 (m110) REVERT: B 640 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8176 (mtpt) REVERT: B 702 GLU cc_start: 0.8096 (mm-30) cc_final: 0.6719 (mp0) REVERT: B 754 THR cc_start: 0.8366 (p) cc_final: 0.7982 (t) REVERT: B 793 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 141 GLU cc_start: 0.8191 (pt0) cc_final: 0.7207 (pp20) REVERT: D 13 LEU cc_start: 0.7402 (mt) cc_final: 0.7056 (tp) REVERT: D 131 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6462 (mp0) REVERT: D 166 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6394 (tmm) REVERT: D 277 ASP cc_start: 0.7626 (m-30) cc_final: 0.7314 (t0) REVERT: D 344 GLU cc_start: 0.6736 (pm20) cc_final: 0.6410 (pm20) REVERT: D 377 ASP cc_start: 0.8120 (t0) cc_final: 0.7507 (m-30) REVERT: D 474 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7693 (tp) REVERT: D 624 GLN cc_start: 0.7963 (mm110) cc_final: 0.7716 (mt0) REVERT: D 653 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7850 (t) REVERT: D 702 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: D 754 THR cc_start: 0.8680 (p) cc_final: 0.8067 (t) outliers start: 49 outliers final: 27 residues processed: 250 average time/residue: 1.1470 time to fit residues: 330.8448 Evaluate side-chains 249 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE 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 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 294 ASN 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 562 ASP Chi-restraints excluded: chain B residue 616 THR 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 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 166 MET Chi-restraints excluded: chain D residue 169 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 151 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 112 optimal weight: 0.0970 chunk 222 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 232 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112238 restraints weight = 76470.448| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.90 r_work: 0.3189 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21673 Z= 0.106 Angle : 0.493 7.224 29528 Z= 0.275 Chirality : 0.040 0.227 3308 Planarity : 0.004 0.057 3659 Dihedral : 13.639 170.837 3494 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.46 % Allowed : 16.24 % Favored : 82.31 % 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: 1.17 (0.17), residues: 2508 helix: 2.62 (0.15), residues: 1183 sheet: -0.96 (0.26), residues: 385 loop : -0.89 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.028 0.001 TYR D 242 PHE 0.018 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 0.00220 / 0.11 (21673) covalent geometry : angle 0.49341 / 0.27 (29528) hydrogen bonds : bond 0.03616 / 2.32 ( 1122) hydrogen bonds : angle 4.31764 / 3.06 ( 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 247 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.114 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 153 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: A 159 MET cc_start: 0.9281 (mmt) cc_final: 0.8855 (mmt) REVERT: A 231 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 306 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: A 416 GLN cc_start: 0.7825 (pp30) cc_final: 0.7534 (pp30) REVERT: A 487 GLU cc_start: 0.8004 (tp30) cc_final: 0.7520 (pt0) REVERT: B 21 LYS cc_start: 0.8614 (mttt) cc_final: 0.8303 (mmmt) REVERT: B 57 LYS cc_start: 0.8286 (tttm) cc_final: 0.7961 (tmtt) REVERT: B 169 PHE cc_start: 0.8128 (p90) cc_final: 0.7818 (p90) REVERT: B 253 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 439 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7903 (mmtm) REVERT: B 640 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8119 (mtpt) REVERT: B 702 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 754 THR cc_start: 0.8320 (p) cc_final: 0.7880 (t) REVERT: C 141 GLU cc_start: 0.8136 (pt0) cc_final: 0.7247 (pp20) REVERT: D 13 LEU cc_start: 0.7397 (mt) cc_final: 0.7060 (tp) REVERT: D 131 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6484 (mp0) REVERT: D 277 ASP cc_start: 0.7639 (m-30) cc_final: 0.7296 (t0) REVERT: D 344 GLU cc_start: 0.6746 (pm20) cc_final: 0.6416 (pm20) REVERT: D 377 ASP cc_start: 0.8114 (t0) cc_final: 0.7518 (m-30) REVERT: D 474 LEU cc_start: 0.7951 (tp) cc_final: 0.7693 (tp) REVERT: D 624 GLN cc_start: 0.7944 (mm110) cc_final: 0.7695 (mt0) REVERT: D 653 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7827 (t) REVERT: D 702 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6885 (mp0) outliers start: 31 outliers final: 21 residues processed: 236 average time/residue: 1.3205 time to fit residues: 358.8387 Evaluate side-chains 234 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE 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 B residue 13 LEU 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 481 ASP Chi-restraints excluded: chain B residue 562 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 C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 230 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 171 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 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 = 0.150698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112531 restraints weight = 76393.129| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.93 r_work: 0.3183 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21673 Z= 0.115 Angle : 0.487 6.640 29528 Z= 0.271 Chirality : 0.040 0.224 3308 Planarity : 0.003 0.050 3659 Dihedral : 13.630 170.658 3494 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 16.66 % Favored : 82.16 % 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: 1.23 (0.17), residues: 2508 helix: 2.66 (0.15), residues: 1183 sheet: -0.92 (0.26), residues: 386 loop : -0.85 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.015 0.001 TYR D 228 PHE 0.018 0.001 PHE D 169 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 0.00245 / 0.11 (21673) covalent geometry : angle 0.48715 / 0.27 (29528) hydrogen bonds : bond 0.03649 / 2.33 ( 1122) hydrogen bonds : angle 4.27611 / 3.03 ( 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 236 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.164 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 153 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: A 159 MET cc_start: 0.9299 (mmt) cc_final: 0.8864 (mmt) REVERT: A 231 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7629 (mp0) REVERT: A 306 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: A 416 GLN cc_start: 0.7845 (pp30) cc_final: 0.7557 (pp30) REVERT: A 487 GLU cc_start: 0.8021 (tp30) cc_final: 0.7522 (pt0) REVERT: B 21 LYS cc_start: 0.8608 (mttt) cc_final: 0.8300 (mmmt) REVERT: B 57 LYS cc_start: 0.8286 (tttm) cc_final: 0.7960 (tmtt) REVERT: B 166 MET cc_start: 0.7258 (tmm) cc_final: 0.6801 (tmm) REVERT: B 169 PHE cc_start: 0.8116 (p90) cc_final: 0.7810 (p90) REVERT: B 253 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 439 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7888 (mmtm) REVERT: B 640 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8119 (mtpt) REVERT: B 702 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 754 THR cc_start: 0.8314 (p) cc_final: 0.7844 (t) REVERT: C 141 GLU cc_start: 0.8146 (pt0) cc_final: 0.7232 (pp20) REVERT: D 13 LEU cc_start: 0.7397 (mt) cc_final: 0.7056 (tp) REVERT: D 131 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6447 (mp0) REVERT: D 166 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6419 (tmm) REVERT: D 242 TYR cc_start: 0.8201 (t80) cc_final: 0.7880 (t80) REVERT: D 277 ASP cc_start: 0.7638 (m-30) cc_final: 0.7295 (t0) REVERT: D 344 GLU cc_start: 0.6773 (pm20) cc_final: 0.6445 (pm20) REVERT: D 377 ASP cc_start: 0.8142 (t0) cc_final: 0.7554 (m-30) REVERT: D 474 LEU cc_start: 0.7965 (tp) cc_final: 0.7710 (tp) REVERT: D 624 GLN cc_start: 0.7933 (mm110) cc_final: 0.7683 (mt0) REVERT: D 653 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7818 (t) REVERT: D 702 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6901 (mp0) outliers start: 25 outliers final: 16 residues processed: 228 average time/residue: 1.3441 time to fit residues: 352.4656 Evaluate side-chains 225 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE 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 B residue 13 LEU 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 481 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 C residue 125 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 702 GLU 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: 1.9990 chunk 112 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 175 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN D 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112151 restraints weight = 76633.480| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.92 r_work: 0.3179 rms_B_bonded: 2.19 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: 0.8598 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21673 Z= 0.122 Angle : 0.493 7.697 29528 Z= 0.273 Chirality : 0.040 0.223 3308 Planarity : 0.004 0.052 3659 Dihedral : 13.634 170.464 3494 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 16.61 % 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: 1.24 (0.17), residues: 2508 helix: 2.68 (0.15), residues: 1178 sheet: -0.90 (0.26), residues: 386 loop : -0.85 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 291 TYR 0.015 0.001 TYR D 228 PHE 0.027 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 0.00265 / 0.12 (21673) covalent geometry : angle 0.49290 / 0.27 (29528) hydrogen bonds : bond 0.03675 / 2.34 ( 1122) hydrogen bonds : angle 4.25058 / 3.01 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12964.16 seconds wall clock time: 219 minutes 34.91 seconds (13174.91 seconds total)