Starting phenix.real_space_refine on Tue May 13 22:41:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h96_34556/05_2025/8h96_34556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h96_34556/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h96_34556/05_2025/8h96_34556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h96_34556/05_2025/8h96_34556.map" model { file = "/net/cci-nas-00/data/ceres_data/8h96_34556/05_2025/8h96_34556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h96_34556/05_2025/8h96_34556.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS: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: 6.47, per 1000 atoms: 0.58 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.46 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: 3.99 Time building geometry restraints manager: 3.03 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- 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 : 5.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP B 525 HIS 0.004 0.001 HIS A 321 PHE 0.026 0.001 PHE B 304 TYR 0.007 0.001 TYR A 513 ARG 0.004 0.000 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.20350 ( 445) hydrogen bonds : angle 6.04085 ( 1278) covalent geometry : bond 0.00410 (11313) covalent geometry : angle 0.68644 (15322) *********************** 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 : 1.226 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: 1.1652 time to fit residues: 161.3574 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 : 1.260 ------------------------------------------------------------------------------- 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 116 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 C 112 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.174518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139605 restraints weight = 14381.982| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.92 r_work: 0.3604 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0866 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= 0.154 Angle : 0.582 6.810 15322 Z= 0.307 Chirality : 0.042 0.149 1764 Planarity : 0.004 0.046 1939 Dihedral : 5.496 52.274 1507 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.00 % Allowed : 14.24 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1395 helix: 1.61 (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 TRP 0.012 0.001 TRP B 525 HIS 0.004 0.001 HIS B 292 PHE 0.017 0.002 PHE B 304 TYR 0.012 0.001 TYR B 577 ARG 0.004 0.000 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 445) hydrogen bonds : angle 4.32069 ( 1278) covalent geometry : bond 0.00364 (11313) covalent geometry : angle 0.58152 (15322) *********************** 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 137 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: C 61 ASP cc_start: 0.8471 (p0) cc_final: 0.8222 (p0) REVERT: C 67 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6509 (mp0) outliers start: 25 outliers final: 11 residues processed: 130 average time/residue: 1.2003 time to fit residues: 169.2920 Evaluate side-chains 120 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 504 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 84 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 A 934 ASN A 950 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.134670 restraints weight = 14708.310| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.89 r_work: 0.3541 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11313 Z= 0.287 Angle : 0.734 8.568 15322 Z= 0.383 Chirality : 0.048 0.174 1764 Planarity : 0.005 0.050 1939 Dihedral : 5.812 55.902 1494 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.52 % Allowed : 16.08 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1395 helix: 1.20 (0.23), residues: 497 sheet: -0.49 (0.32), residues: 293 loop : -2.12 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 525 HIS 0.007 0.002 HIS A 814 PHE 0.026 0.002 PHE B 157 TYR 0.017 0.002 TYR B 577 ARG 0.005 0.001 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.06464 ( 445) hydrogen bonds : angle 4.61161 ( 1278) covalent geometry : bond 0.00708 (11313) covalent geometry : angle 0.73402 (15322) *********************** 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 152 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6722 (ptm-80) REVERT: A 649 ASP cc_start: 0.8360 (t0) cc_final: 0.8154 (t0) REVERT: B 435 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8696 (tt) outliers start: 44 outliers final: 23 residues processed: 143 average time/residue: 1.1835 time to fit residues: 183.9366 Evaluate side-chains 129 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 401 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 135 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 A 934 ASN B 292 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142444 restraints weight = 14500.903| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.96 r_work: 0.3651 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11313 Z= 0.097 Angle : 0.495 8.661 15322 Z= 0.260 Chirality : 0.039 0.144 1764 Planarity : 0.003 0.045 1939 Dihedral : 4.915 53.419 1494 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.40 % Allowed : 18.16 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1395 helix: 1.84 (0.23), residues: 504 sheet: -0.40 (0.33), residues: 288 loop : -1.90 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 525 HIS 0.003 0.001 HIS B 537 PHE 0.015 0.001 PHE B 157 TYR 0.017 0.001 TYR A 247 ARG 0.005 0.000 ARG A 764 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 445) hydrogen bonds : angle 3.82889 ( 1278) covalent geometry : bond 0.00214 (11313) covalent geometry : angle 0.49476 (15322) *********************** 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 144 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8238 (t80) cc_final: 0.7988 (t80) REVERT: A 186 GLU cc_start: 0.8133 (mp0) cc_final: 0.7730 (pm20) REVERT: A 214 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6750 (mtm-85) REVERT: A 250 MET cc_start: 0.8036 (tpp) cc_final: 0.7792 (mmp) REVERT: A 349 ARG cc_start: 0.8165 (mpp-170) cc_final: 0.7735 (mtm-85) REVERT: A 763 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7518 (p0) REVERT: C 67 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6502 (mp0) outliers start: 30 outliers final: 9 residues processed: 136 average time/residue: 1.1376 time to fit residues: 168.2774 Evaluate side-chains 118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 503 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 67 GLU 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 45 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139931 restraints weight = 14456.157| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.90 r_work: 0.3616 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11313 Z= 0.124 Angle : 0.539 9.277 15322 Z= 0.279 Chirality : 0.040 0.141 1764 Planarity : 0.004 0.045 1939 Dihedral : 4.988 54.102 1494 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.64 % Allowed : 18.72 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1395 helix: 1.92 (0.23), residues: 501 sheet: -0.44 (0.32), residues: 288 loop : -1.87 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 525 HIS 0.005 0.001 HIS B 537 PHE 0.013 0.001 PHE B 157 TYR 0.016 0.001 TYR A 247 ARG 0.003 0.000 ARG A 764 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 445) hydrogen bonds : angle 3.89565 ( 1278) covalent geometry : bond 0.00291 (11313) covalent geometry : angle 0.53940 (15322) *********************** 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 138 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8097 (mp0) cc_final: 0.7721 (pm20) REVERT: A 214 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6731 (mtm-85) REVERT: A 417 GLU cc_start: 0.7801 (pm20) cc_final: 0.7570 (tp30) REVERT: C 67 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6484 (mp0) outliers start: 33 outliers final: 16 residues processed: 130 average time/residue: 1.1509 time to fit residues: 162.8996 Evaluate side-chains 124 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 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 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 56 ARG 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 124 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 B 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.172844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138264 restraints weight = 14600.389| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.90 r_work: 0.3587 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11313 Z= 0.164 Angle : 0.588 9.480 15322 Z= 0.304 Chirality : 0.042 0.144 1764 Planarity : 0.004 0.046 1939 Dihedral : 5.219 55.093 1494 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.16 % Allowed : 19.36 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1395 helix: 1.71 (0.23), residues: 507 sheet: -0.50 (0.32), residues: 293 loop : -1.96 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 525 HIS 0.006 0.001 HIS B 292 PHE 0.015 0.002 PHE A 173 TYR 0.014 0.001 TYR B 577 ARG 0.004 0.000 ARG A 764 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 445) hydrogen bonds : angle 4.03027 ( 1278) covalent geometry : bond 0.00398 (11313) covalent geometry : angle 0.58753 (15322) *********************** 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 137 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8105 (mp0) cc_final: 0.7722 (pm20) REVERT: A 214 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6764 (mtm-85) REVERT: A 417 GLU cc_start: 0.7798 (pm20) cc_final: 0.7543 (tp30) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 1.1921 time to fit residues: 169.6091 Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 489 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 403 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.172687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138101 restraints weight = 14706.061| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.91 r_work: 0.3591 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11313 Z= 0.155 Angle : 0.580 9.882 15322 Z= 0.300 Chirality : 0.042 0.143 1764 Planarity : 0.004 0.046 1939 Dihedral : 5.229 55.391 1494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.88 % Allowed : 19.12 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1395 helix: 1.70 (0.23), residues: 507 sheet: -0.56 (0.32), residues: 293 loop : -1.98 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 525 HIS 0.004 0.001 HIS B 537 PHE 0.015 0.001 PHE A 173 TYR 0.014 0.001 TYR A 247 ARG 0.003 0.000 ARG A 764 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 445) hydrogen bonds : angle 4.02237 ( 1278) covalent geometry : bond 0.00374 (11313) covalent geometry : angle 0.58043 (15322) *********************** 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 144 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8116 (mp0) cc_final: 0.7734 (pm20) REVERT: A 214 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6778 (mtm-85) REVERT: A 250 MET cc_start: 0.8182 (tpp) cc_final: 0.7908 (mmp) REVERT: A 349 ARG cc_start: 0.8208 (mpp-170) cc_final: 0.7898 (mpp-170) REVERT: A 764 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7627 (mmm160) outliers start: 36 outliers final: 26 residues processed: 136 average time/residue: 1.2040 time to fit residues: 177.9193 Evaluate side-chains 134 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 248 ILE 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 429 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1007 CYS 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 403 LEU Chi-restraints excluded: chain B residue 456 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140224 restraints weight = 14598.863| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.91 r_work: 0.3633 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11313 Z= 0.114 Angle : 0.537 10.319 15322 Z= 0.278 Chirality : 0.040 0.139 1764 Planarity : 0.004 0.045 1939 Dihedral : 5.028 54.804 1494 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.32 % Allowed : 20.64 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1395 helix: 1.86 (0.23), residues: 509 sheet: -0.56 (0.32), residues: 293 loop : -1.93 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 167 HIS 0.005 0.001 HIS B 537 PHE 0.012 0.001 PHE A 173 TYR 0.015 0.001 TYR A 247 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 445) hydrogen bonds : angle 3.85185 ( 1278) covalent geometry : bond 0.00265 (11313) covalent geometry : angle 0.53715 (15322) *********************** 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 138 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8122 (mp0) cc_final: 0.7705 (pm20) REVERT: A 214 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6749 (mtm-85) REVERT: A 250 MET cc_start: 0.8071 (tpp) cc_final: 0.7821 (mmp) REVERT: A 349 ARG cc_start: 0.8150 (mpp-170) cc_final: 0.7853 (mpp-170) REVERT: A 417 GLU cc_start: 0.7734 (pm20) cc_final: 0.7388 (tp30) REVERT: A 764 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7533 (mmm160) REVERT: A 893 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: B 401 MET cc_start: 0.8110 (ptp) cc_final: 0.7766 (pmm) outliers start: 29 outliers final: 21 residues processed: 134 average time/residue: 1.1550 time to fit residues: 168.4561 Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU 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 403 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 0.0980 chunk 115 optimal weight: 0.0050 chunk 96 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 341 GLN A 425 HIS A 535 ASN A 617 GLN A 763 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.179032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.144570 restraints weight = 14534.993| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.93 r_work: 0.3688 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11313 Z= 0.091 Angle : 0.501 11.268 15322 Z= 0.258 Chirality : 0.039 0.172 1764 Planarity : 0.003 0.044 1939 Dihedral : 4.597 53.116 1494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.92 % Allowed : 21.12 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1395 helix: 2.04 (0.23), residues: 515 sheet: -0.49 (0.32), residues: 283 loop : -1.87 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 167 HIS 0.004 0.001 HIS B 537 PHE 0.009 0.001 PHE A 173 TYR 0.016 0.001 TYR A 247 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.02583 ( 445) hydrogen bonds : angle 3.57493 ( 1278) covalent geometry : bond 0.00200 (11313) covalent geometry : angle 0.50092 (15322) *********************** 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 136 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.295 Fit side-chains REVERT: A 186 GLU cc_start: 0.8163 (mp0) cc_final: 0.7741 (pm20) REVERT: A 214 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6614 (mtm-85) REVERT: A 241 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7889 (mttp) REVERT: A 250 MET cc_start: 0.7927 (tpp) cc_final: 0.7685 (mmp) REVERT: A 349 ARG cc_start: 0.8074 (mpp-170) cc_final: 0.7843 (mpp-170) REVERT: A 417 GLU cc_start: 0.7735 (pm20) cc_final: 0.7343 (tp30) REVERT: A 763 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7235 (p0) REVERT: A 893 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 172 ASP cc_start: 0.7892 (m-30) cc_final: 0.7530 (m-30) REVERT: B 401 MET cc_start: 0.8070 (ptp) cc_final: 0.7742 (pmm) outliers start: 24 outliers final: 13 residues processed: 133 average time/residue: 1.1296 time to fit residues: 163.8376 Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 763 ASN 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 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 13 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.0570 chunk 104 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138215 restraints weight = 14583.402| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.90 r_work: 0.3591 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11313 Z= 0.168 Angle : 0.614 11.817 15322 Z= 0.315 Chirality : 0.042 0.187 1764 Planarity : 0.004 0.046 1939 Dihedral : 4.934 55.638 1491 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.00 % Allowed : 21.12 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1395 helix: 1.84 (0.23), residues: 507 sheet: -0.54 (0.32), residues: 294 loop : -1.95 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 167 HIS 0.004 0.001 HIS A1039 PHE 0.013 0.001 PHE A 173 TYR 0.015 0.001 TYR B 577 ARG 0.003 0.000 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 445) hydrogen bonds : angle 3.98870 ( 1278) covalent geometry : bond 0.00409 (11313) covalent geometry : angle 0.61431 (15322) ********************** 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 131 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6592 (mtm-85) REVERT: A 241 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7891 (mttp) REVERT: A 250 MET cc_start: 0.8126 (tpp) cc_final: 0.7862 (mmp) REVERT: A 349 ARG cc_start: 0.8173 (mpp-170) cc_final: 0.7842 (mpp-170) REVERT: A 417 GLU cc_start: 0.7760 (pm20) cc_final: 0.7407 (tp30) REVERT: A 893 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7805 (mp0) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 1.1618 time to fit residues: 161.1504 Evaluate side-chains 124 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 763 ASN 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 456 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 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.138064 restraints weight = 14622.930| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.91 r_work: 0.3602 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11313 Z= 0.165 Angle : 0.614 11.781 15322 Z= 0.315 Chirality : 0.042 0.198 1764 Planarity : 0.004 0.046 1939 Dihedral : 4.999 55.814 1491 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.84 % Allowed : 21.92 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1395 helix: 1.76 (0.23), residues: 505 sheet: -0.57 (0.31), residues: 302 loop : -1.96 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 167 HIS 0.005 0.001 HIS A 144 PHE 0.013 0.001 PHE A 173 TYR 0.014 0.001 TYR B 577 ARG 0.003 0.000 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 445) hydrogen bonds : angle 4.01758 ( 1278) covalent geometry : bond 0.00401 (11313) covalent geometry : angle 0.61429 (15322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6407.84 seconds wall clock time: 111 minutes 19.02 seconds (6679.02 seconds total)