Starting phenix.real_space_refine on Sat Aug 23 09:07:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h96_34556/08_2025/8h96_34556.map" } resolution = 2.78 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= 0.005 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 7057 2.51 5 N 1898 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7481 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 2.65, per 1000 atoms: 0.24 Number of scatterers: 11098 At special positions: 0 Unit cell: (90.2, 102.3, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2052 8.00 N 1898 7.00 C 7057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 636.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 41.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.008A pdb=" N LEU A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.478A pdb=" N VAL A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.756A pdb=" N ASP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 227 " --> pdb=" O ASP A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.859A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.863A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.744A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.833A pdb=" N GLN A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 356 through 373 removed outlier: 3.513A pdb=" N THR A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.814A pdb=" N TYR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.542A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.057A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 467 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 468' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.500A pdb=" N THR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.934A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.518A pdb=" N GLU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.859A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.713A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 693 removed outlier: 4.069A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.576A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 removed outlier: 3.752A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.884A pdb=" N GLY A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 removed outlier: 3.689A pdb=" N LEU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 936 through 949 removed outlier: 3.667A pdb=" N GLY A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.832A pdb=" N CYS A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.712A pdb=" N GLU A1021 " --> pdb=" O TRP A1018 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1022' Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.616A pdb=" N ALA A1048 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1045 through 1049' Processing helix chain 'B' and resid 157 through 174 removed outlier: 3.640A pdb=" N GLU B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 171 " --> pdb=" O TRP B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.545A pdb=" N GLU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 41' Processing helix chain 'C' and resid 51 through 58 removed outlier: 4.130A pdb=" N GLU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.128A pdb=" N ILE A 175 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP A 220 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 177 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432 Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 571 removed outlier: 6.636A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 787 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 844 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 872 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 901 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 929 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 986 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.953A pdb=" N LEU B 284 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS B 580 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS B 286 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS B 578 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 288 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B 556 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.707A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 351 removed outlier: 6.717A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.624A pdb=" N VAL B 411 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN B 424 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 420 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 437 removed outlier: 3.546A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 460 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 476 removed outlier: 6.435A pdb=" N GLY B 486 " --> pdb=" O MET B 472 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 474 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N HIS B 476 " --> pdb=" O TRP B 482 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TRP B 482 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.472A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 445 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2185 1.33 - 1.45: 2556 1.45 - 1.57: 6444 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 11313 Sorted by residual: bond pdb=" C HIS A 231 " pdb=" N ASP A 232 " ideal model delta sigma weight residual 1.334 1.520 -0.187 1.30e-02 5.92e+03 2.06e+02 bond pdb=" N VAL B 301 " pdb=" CA VAL B 301 " ideal model delta sigma weight residual 1.452 1.511 -0.058 1.18e-02 7.18e+03 2.45e+01 bond pdb=" C SER A 210 " pdb=" N GLN A 211 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.19e+01 bond pdb=" CE1 HIS A 848 " pdb=" NE2 HIS A 848 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" N VAL B 299 " pdb=" CA VAL B 299 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.14e-02 7.69e+03 1.49e+01 ... (remaining 11308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 15270 4.22 - 8.44: 47 8.44 - 12.66: 3 12.66 - 16.89: 0 16.89 - 21.11: 2 Bond angle restraints: 15322 Sorted by residual: angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta sigma weight residual 110.22 89.11 21.11 1.63e+00 3.76e-01 1.68e+02 angle pdb=" N GLY A 221 " pdb=" CA GLY A 221 " pdb=" C GLY A 221 " ideal model delta sigma weight residual 113.18 131.09 -17.91 2.37e+00 1.78e-01 5.71e+01 angle pdb=" N VAL B 301 " pdb=" CA VAL B 301 " pdb=" C VAL B 301 " ideal model delta sigma weight residual 112.96 118.84 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" C ASP A 853 " pdb=" CA ASP A 853 " pdb=" CB ASP A 853 " ideal model delta sigma weight residual 117.23 109.41 7.82 1.36e+00 5.41e-01 3.30e+01 angle pdb=" CA PHE B 304 " pdb=" CB PHE B 304 " pdb=" CG PHE B 304 " ideal model delta sigma weight residual 113.80 119.11 -5.31 1.00e+00 1.00e+00 2.82e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5895 17.33 - 34.65: 716 34.65 - 51.98: 185 51.98 - 69.31: 35 69.31 - 86.64: 18 Dihedral angle restraints: 6849 sinusoidal: 2750 harmonic: 4099 Sorted by residual: dihedral pdb=" N LEU A 222 " pdb=" C LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta harmonic sigma weight residual 122.80 95.81 26.99 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" C LEU A 222 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" CD ARG A 843 " pdb=" NE ARG A 843 " pdb=" CZ ARG A 843 " pdb=" NH1 ARG A 843 " ideal model delta sinusoidal sigma weight residual 0.00 36.61 -36.61 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1698 0.103 - 0.206: 60 0.206 - 0.309: 5 0.309 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA LEU A 222 " pdb=" N LEU A 222 " pdb=" C LEU A 222 " pdb=" CB LEU A 222 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASN A 847 " pdb=" N ASN A 847 " pdb=" C ASN A 847 " pdb=" CB ASN A 847 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 851 " pdb=" N ILE A 851 " pdb=" C ILE A 851 " pdb=" CB ILE A 851 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1761 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 843 " 0.654 9.50e-02 1.11e+02 2.93e-01 5.23e+01 pdb=" NE ARG A 843 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 843 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 843 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 843 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 847 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C ASN A 847 " 0.063 2.00e-02 2.50e+03 pdb=" O ASN A 847 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS A 848 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 649 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ASP A 649 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP A 649 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 650 " -0.014 2.00e-02 2.50e+03 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1605 2.76 - 3.29: 9825 3.29 - 3.83: 16829 3.83 - 4.36: 19707 4.36 - 4.90: 36055 Nonbonded interactions: 84021 Sorted by model distance: nonbonded pdb=" N GLU B 387 " pdb=" OE1 GLU B 387 " model vdw 2.225 3.120 nonbonded pdb=" OE1 GLU A 396 " pdb=" OH TYR A 413 " model vdw 2.260 3.040 nonbonded pdb=" OG SER A 538 " pdb=" OD2 ASP A 541 " model vdw 2.279 3.040 nonbonded pdb=" O CYS A 906 " pdb=" ND2 ASN A 934 " model vdw 2.281 3.120 nonbonded pdb=" O HIS A 367 " pdb=" OG1 THR A 370 " model vdw 2.285 3.040 ... (remaining 84016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.004 0.187 11313 Z= 0.252 Angle : 0.686 21.106 15322 Z= 0.407 Chirality : 0.046 0.516 1764 Planarity : 0.008 0.293 1939 Dihedral : 16.703 86.635 4177 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.52 % Allowed : 14.16 % Favored : 84.32 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -0.55 (0.22), residues: 1395 helix: 1.41 (0.23), residues: 495 sheet: -0.39 (0.33), residues: 279 loop : -1.87 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.007 0.001 TYR A 513 PHE 0.026 0.001 PHE B 304 TRP 0.010 0.001 TRP B 525 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00410 (11313) covalent geometry : angle 0.68644 (15322) hydrogen bonds : bond 0.20350 ( 445) hydrogen bonds : angle 6.04085 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: B 152 ASP cc_start: 0.3498 (OUTLIER) cc_final: 0.3041 (m-30) REVERT: B 401 MET cc_start: 0.8112 (ptp) cc_final: 0.7898 (pmm) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.6377 time to fit residues: 87.4799 Evaluate side-chains 122 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 303 ASN A 321 HIS A 425 HIS A 431 GLN A 535 ASN A 763 ASN B 292 HIS B 419 GLN C 112 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.174452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139533 restraints weight = 14510.634| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.94 r_work: 0.3603 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11313 Z= 0.156 Angle : 0.582 6.721 15322 Z= 0.307 Chirality : 0.042 0.149 1764 Planarity : 0.004 0.047 1939 Dihedral : 5.496 52.455 1507 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.08 % Allowed : 14.24 % Favored : 83.68 % 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 aren not related in a simple way. whole: -0.45 (0.22), residues: 1395 helix: 1.60 (0.23), residues: 501 sheet: -0.37 (0.33), residues: 287 loop : -1.96 (0.22), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.013 0.001 TYR B 577 PHE 0.019 0.002 PHE B 304 TRP 0.012 0.001 TRP B 525 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00366 (11313) covalent geometry : angle 0.58227 (15322) hydrogen bonds : bond 0.05022 ( 445) hydrogen bonds : angle 4.31660 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6514 (mp0) outliers start: 26 outliers final: 10 residues processed: 130 average time/residue: 0.6285 time to fit residues: 88.2817 Evaluate side-chains 118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 535 ASN A 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.179397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144618 restraints weight = 14573.647| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.96 r_work: 0.3686 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11313 Z= 0.090 Angle : 0.478 7.713 15322 Z= 0.251 Chirality : 0.039 0.141 1764 Planarity : 0.003 0.042 1939 Dihedral : 4.626 50.817 1494 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.76 % Allowed : 16.24 % Favored : 82.00 % 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 aren not related in a simple way. whole: -0.09 (0.23), residues: 1395 helix: 2.11 (0.24), residues: 498 sheet: -0.37 (0.33), residues: 279 loop : -1.81 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.009 0.001 TYR A 251 PHE 0.018 0.001 PHE B 157 TRP 0.010 0.001 TRP B 525 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00190 (11313) covalent geometry : angle 0.47819 (15322) hydrogen bonds : bond 0.02940 ( 445) hydrogen bonds : angle 3.76235 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8128 (mp0) cc_final: 0.7728 (pm20) REVERT: A 214 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6532 (mtm-85) REVERT: A 250 MET cc_start: 0.7873 (tpp) cc_final: 0.7657 (mmp) REVERT: A 349 ARG cc_start: 0.8171 (mpp-170) cc_final: 0.7691 (mtm-85) REVERT: A 417 GLU cc_start: 0.7871 (pm20) cc_final: 0.7616 (tp30) REVERT: A 649 ASP cc_start: 0.7855 (t0) cc_final: 0.7500 (t0) REVERT: A 924 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8458 (ptmm) REVERT: C 61 ASP cc_start: 0.8426 (p0) cc_final: 0.8215 (p0) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 0.5803 time to fit residues: 87.1945 Evaluate side-chains 118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 535 ASN A 763 ASN A 950 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.171807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.137110 restraints weight = 14731.764| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.90 r_work: 0.3571 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11313 Z= 0.210 Angle : 0.639 8.677 15322 Z= 0.332 Chirality : 0.044 0.147 1764 Planarity : 0.004 0.046 1939 Dihedral : 5.295 54.119 1493 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.12 % Allowed : 15.92 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.23), residues: 1395 helix: 1.65 (0.23), residues: 501 sheet: -0.40 (0.32), residues: 293 loop : -1.95 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.015 0.002 TYR B 577 PHE 0.020 0.002 PHE B 157 TRP 0.013 0.001 TRP B 525 HIS 0.008 0.002 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00513 (11313) covalent geometry : angle 0.63873 (15322) hydrogen bonds : bond 0.05314 ( 445) hydrogen bonds : angle 4.24993 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8330 (t80) cc_final: 0.7327 (m-80) REVERT: A 186 GLU cc_start: 0.8082 (mp0) cc_final: 0.7712 (pm20) REVERT: A 214 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6802 (mtm-85) REVERT: A 349 ARG cc_start: 0.8221 (mpp-170) cc_final: 0.7797 (mtm-85) outliers start: 39 outliers final: 17 residues processed: 141 average time/residue: 0.6213 time to fit residues: 94.9079 Evaluate side-chains 128 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 466 GLN A 535 ASN A 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.136417 restraints weight = 14690.812| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.88 r_work: 0.3571 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11313 Z= 0.209 Angle : 0.640 8.791 15322 Z= 0.334 Chirality : 0.044 0.146 1764 Planarity : 0.004 0.047 1939 Dihedral : 5.406 54.756 1493 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.72 % Allowed : 17.68 % Favored : 79.60 % 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 aren not related in a simple way. whole: -0.58 (0.22), residues: 1395 helix: 1.54 (0.23), residues: 498 sheet: -0.55 (0.32), residues: 293 loop : -2.00 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.014 0.002 TYR B 577 PHE 0.019 0.002 PHE B 157 TRP 0.013 0.002 TRP B 525 HIS 0.007 0.002 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00513 (11313) covalent geometry : angle 0.63970 (15322) hydrogen bonds : bond 0.05210 ( 445) hydrogen bonds : angle 4.24190 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8268 (t80) cc_final: 0.7253 (m-80) REVERT: A 214 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (mtm-85) REVERT: A 763 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8087 (p0) REVERT: B 435 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8760 (tt) REVERT: C 61 ASP cc_start: 0.8396 (p0) cc_final: 0.8188 (p0) REVERT: C 71 MET cc_start: 0.8006 (mmm) cc_final: 0.7628 (mmt) outliers start: 34 outliers final: 20 residues processed: 135 average time/residue: 0.6443 time to fit residues: 93.9127 Evaluate side-chains 127 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 136 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 466 GLN A 535 ASN A 617 GLN B 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.144130 restraints weight = 14623.309| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.89 r_work: 0.3668 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11313 Z= 0.092 Angle : 0.500 9.961 15322 Z= 0.260 Chirality : 0.039 0.140 1764 Planarity : 0.003 0.044 1939 Dihedral : 4.715 52.212 1493 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.16 % Allowed : 18.96 % Favored : 78.88 % 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 aren not related in a simple way. whole: -0.22 (0.23), residues: 1395 helix: 1.99 (0.23), residues: 504 sheet: -0.49 (0.32), residues: 284 loop : -1.90 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.017 0.001 TYR A 247 PHE 0.009 0.001 PHE B 157 TRP 0.011 0.001 TRP A 629 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00202 (11313) covalent geometry : angle 0.50024 (15322) hydrogen bonds : bond 0.02726 ( 445) hydrogen bonds : angle 3.68030 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8203 (t80) cc_final: 0.7213 (m-80) REVERT: A 186 GLU cc_start: 0.8133 (mp0) cc_final: 0.7771 (pm20) REVERT: A 214 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6672 (mtm-85) REVERT: A 250 MET cc_start: 0.8069 (tpp) cc_final: 0.7837 (mmp) REVERT: A 346 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5774 (tp) REVERT: A 349 ARG cc_start: 0.8093 (mpp-170) cc_final: 0.7755 (mpp-170) REVERT: A 417 GLU cc_start: 0.7762 (pm20) cc_final: 0.7518 (tp30) REVERT: A 617 GLN cc_start: 0.2465 (OUTLIER) cc_final: 0.2263 (pm20) REVERT: C 61 ASP cc_start: 0.8474 (p0) cc_final: 0.8239 (p0) outliers start: 27 outliers final: 11 residues processed: 134 average time/residue: 0.6039 time to fit residues: 87.9243 Evaluate side-chains 122 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 425 HIS A 535 ASN A 617 GLN B 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.140676 restraints weight = 14625.357| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.91 r_work: 0.3626 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11313 Z= 0.119 Angle : 0.537 9.962 15322 Z= 0.278 Chirality : 0.040 0.141 1764 Planarity : 0.004 0.044 1939 Dihedral : 4.818 53.019 1493 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.16 % Allowed : 19.28 % Favored : 78.56 % 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 aren not related in a simple way. whole: -0.18 (0.23), residues: 1395 helix: 1.96 (0.23), residues: 510 sheet: -0.48 (0.32), residues: 289 loop : -1.86 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.017 0.001 TYR A 247 PHE 0.011 0.001 PHE B 157 TRP 0.011 0.001 TRP B 167 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00277 (11313) covalent geometry : angle 0.53665 (15322) hydrogen bonds : bond 0.03577 ( 445) hydrogen bonds : angle 3.77826 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8191 (t80) cc_final: 0.7163 (m-80) REVERT: A 186 GLU cc_start: 0.8111 (mp0) cc_final: 0.7737 (pm20) REVERT: A 213 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8111 (tp30) REVERT: A 214 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6799 (mtm-85) REVERT: A 289 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: A 346 LEU cc_start: 0.6178 (tp) cc_final: 0.5805 (tp) REVERT: A 349 ARG cc_start: 0.8076 (mpp-170) cc_final: 0.7739 (mpp-170) REVERT: A 417 GLU cc_start: 0.7756 (pm20) cc_final: 0.7482 (tp30) outliers start: 27 outliers final: 16 residues processed: 132 average time/residue: 0.6326 time to fit residues: 90.4657 Evaluate side-chains 131 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 425 HIS A 535 ASN B 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.180432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146152 restraints weight = 14530.023| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.92 r_work: 0.3701 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11313 Z= 0.084 Angle : 0.480 10.448 15322 Z= 0.247 Chirality : 0.038 0.141 1764 Planarity : 0.003 0.043 1939 Dihedral : 4.394 50.760 1493 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.00 % Allowed : 20.08 % Favored : 77.92 % 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 aren not related in a simple way. whole: -0.04 (0.23), residues: 1395 helix: 2.20 (0.24), residues: 509 sheet: -0.44 (0.32), residues: 279 loop : -1.85 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.017 0.001 TYR A 247 PHE 0.009 0.001 PHE A 858 TRP 0.010 0.001 TRP B 525 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00184 (11313) covalent geometry : angle 0.47986 (15322) hydrogen bonds : bond 0.02372 ( 445) hydrogen bonds : angle 3.46715 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8187 (t80) cc_final: 0.7163 (m-80) REVERT: A 186 GLU cc_start: 0.8167 (mp0) cc_final: 0.7775 (pm20) REVERT: A 214 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6721 (mtm-85) REVERT: A 250 MET cc_start: 0.7940 (tpp) cc_final: 0.7633 (mmp) REVERT: A 289 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 346 LEU cc_start: 0.6062 (tp) cc_final: 0.5780 (tp) REVERT: A 349 ARG cc_start: 0.8045 (mpp-170) cc_final: 0.7733 (mpp-170) REVERT: A 417 GLU cc_start: 0.7766 (pm20) cc_final: 0.7421 (tp30) REVERT: A 893 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 172 ASP cc_start: 0.8000 (m-30) cc_final: 0.7642 (m-30) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.6166 time to fit residues: 91.0557 Evaluate side-chains 125 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 120 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 341 GLN A 425 HIS A 535 ASN B 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.175820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141295 restraints weight = 14413.083| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.90 r_work: 0.3627 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11313 Z= 0.126 Angle : 0.552 11.159 15322 Z= 0.283 Chirality : 0.040 0.175 1764 Planarity : 0.003 0.044 1939 Dihedral : 4.561 51.864 1491 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.08 % Allowed : 20.08 % Favored : 77.84 % 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 aren not related in a simple way. whole: -0.05 (0.23), residues: 1395 helix: 2.15 (0.23), residues: 503 sheet: -0.47 (0.32), residues: 294 loop : -1.79 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1027 TYR 0.015 0.001 TYR A 247 PHE 0.010 0.001 PHE A 693 TRP 0.023 0.001 TRP B 167 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00299 (11313) covalent geometry : angle 0.55249 (15322) hydrogen bonds : bond 0.03631 ( 445) hydrogen bonds : angle 3.75113 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8283 (t80) cc_final: 0.7211 (m-80) REVERT: A 186 GLU cc_start: 0.8148 (mp0) cc_final: 0.7756 (pm20) REVERT: A 244 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6609 (tp40) REVERT: A 289 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: A 346 LEU cc_start: 0.6108 (tp) cc_final: 0.5777 (tp) REVERT: A 349 ARG cc_start: 0.8102 (mpp-170) cc_final: 0.7736 (mpp-170) REVERT: A 893 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: B 172 ASP cc_start: 0.8089 (m-30) cc_final: 0.7720 (m-30) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 0.6390 time to fit residues: 91.2332 Evaluate side-chains 128 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 0.0670 chunk 63 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 425 HIS A 535 ASN B 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.179798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145559 restraints weight = 14476.162| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.89 r_work: 0.3697 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11313 Z= 0.093 Angle : 0.520 11.359 15322 Z= 0.265 Chirality : 0.039 0.183 1764 Planarity : 0.003 0.043 1939 Dihedral : 4.271 49.769 1491 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.44 % Allowed : 21.28 % Favored : 77.28 % 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 aren not related in a simple way. whole: -0.00 (0.23), residues: 1395 helix: 2.18 (0.23), residues: 509 sheet: -0.44 (0.32), residues: 284 loop : -1.78 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.016 0.001 TYR A 247 PHE 0.008 0.001 PHE A 858 TRP 0.023 0.001 TRP B 167 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00208 (11313) covalent geometry : angle 0.52041 (15322) hydrogen bonds : bond 0.02617 ( 445) hydrogen bonds : angle 3.53882 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8183 (t80) cc_final: 0.7089 (m-80) REVERT: A 186 GLU cc_start: 0.8142 (mp0) cc_final: 0.7728 (pm20) REVERT: A 214 ARG cc_start: 0.6971 (ptm-80) cc_final: 0.6225 (mmt-90) REVERT: A 289 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: A 346 LEU cc_start: 0.5986 (tp) cc_final: 0.5689 (tp) REVERT: A 349 ARG cc_start: 0.8021 (mpp-170) cc_final: 0.7683 (mpp-170) REVERT: A 417 GLU cc_start: 0.7723 (pm20) cc_final: 0.7278 (tp30) REVERT: A 893 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: B 172 ASP cc_start: 0.7655 (m-30) cc_final: 0.7324 (m-30) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.6338 time to fit residues: 90.5790 Evaluate side-chains 129 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 425 HIS A 535 ASN B 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.140232 restraints weight = 14616.810| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.90 r_work: 0.3617 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11313 Z= 0.137 Angle : 0.585 11.738 15322 Z= 0.298 Chirality : 0.041 0.195 1764 Planarity : 0.004 0.043 1939 Dihedral : 4.652 50.958 1491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.68 % Allowed : 20.88 % Favored : 77.44 % 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 aren not related in a simple way. whole: -0.10 (0.23), residues: 1395 helix: 2.06 (0.23), residues: 503 sheet: -0.49 (0.32), residues: 295 loop : -1.77 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.014 0.001 TYR A 247 PHE 0.011 0.001 PHE A 693 TRP 0.031 0.001 TRP B 167 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00329 (11313) covalent geometry : angle 0.58535 (15322) hydrogen bonds : bond 0.03884 ( 445) hydrogen bonds : angle 3.83780 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.43 seconds wall clock time: 60 minutes 37.22 seconds (3637.22 seconds total)