Starting phenix.real_space_refine on Tue Jul 29 06:40:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.map" model { file = "/net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h95_34555/07_2025/8h95_34555.cif" } resolution = 3.38 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= 0.000 sd= 0.036 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 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.40, per 1000 atoms: 0.67 Number of scatterers: 11098 At special positions: 0 Unit cell: (92.4, 105.6, 132, 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: 2.83 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: 48 helices and 14 sheets defined 40.1% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.639A pdb=" N LYS A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.678A pdb=" N LEU A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 202 through 211 removed outlier: 4.595A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.854A pdb=" N ASP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.584A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.637A pdb=" N ARG A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.751A 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: 3.534A pdb=" N LEU A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.920A 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: 3.575A pdb=" N TYR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.529A pdb=" N ILE A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.896A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.010A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 518 through 532 removed outlier: 4.103A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.580A 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: 4.217A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.558A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.717A pdb=" N MET A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) 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: 3.974A 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: 3.825A 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: 3.895A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 865 removed outlier: 4.467A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 removed outlier: 3.887A pdb=" N MET A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 936 through 951 removed outlier: 3.872A pdb=" N GLY A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A 951 " --> pdb=" O GLY A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.753A 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 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.697A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 174 removed outlier: 3.503A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.589A pdb=" N VAL C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 42 " --> pdb=" O GLN C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 38 through 42' Processing helix chain 'C' and resid 51 through 59 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: 5.981A pdb=" N ILE A 175 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP A 220 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 177 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 140 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 286 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 142 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL A 288 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS A 144 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 28 " --> pdb=" O GLU A 289 " (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: 3.630A pdb=" N ILE A 594 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 596 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 675 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A 701 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 758 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 814 through 816 removed outlier: 7.110A pdb=" N LEU A 815 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 873 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 901 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 929 " --> pdb=" O GLY A 959 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 Processing sheet with id=AA7, first strand: chain 'B' and resid 283 through 288 removed outlier: 3.645A pdb=" N ALA B 283 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B 576 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 566 " --> pdb=" O TYR B 577 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 300 removed outlier: 4.021A pdb=" N VAL B 298 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 308 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 318 " --> pdb=" O SER B 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 351 removed outlier: 7.057A pdb=" N GLY B 361 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS B 349 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B 359 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU B 351 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR B 357 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 372 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR B 379 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 394 through 397 removed outlier: 4.241A pdb=" N MET B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 411 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN B 424 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 434 through 437 removed outlier: 3.747A pdb=" N ASN B 434 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 476 removed outlier: 3.597A pdb=" N SER B 473 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 504 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.359A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.757A pdb=" N MET C 49 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 75 " --> pdb=" O PHE C 92 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1227 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: 4.35 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3515 1.34 - 1.46: 1583 1.46 - 1.58: 6087 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 11313 Sorted by residual: bond pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.82e+00 bond pdb=" CA ARG A 214 " pdb=" CB ARG A 214 " ideal model delta sigma weight residual 1.530 1.575 -0.045 1.57e-02 4.06e+03 8.27e+00 bond pdb=" N TRP B 151 " pdb=" CA TRP B 151 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.19e+00 bond pdb=" N GLN B 148 " pdb=" CA GLN B 148 " ideal model delta sigma weight residual 1.451 1.485 -0.034 1.70e-02 3.46e+03 4.10e+00 bond pdb=" C ASP B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.30e-02 5.92e+03 2.65e+00 ... (remaining 11308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 15249 4.16 - 8.32: 68 8.32 - 12.48: 2 12.48 - 16.64: 1 16.64 - 20.80: 2 Bond angle restraints: 15322 Sorted by residual: angle pdb=" N ASP A 854 " pdb=" CA ASP A 854 " pdb=" C ASP A 854 " ideal model delta sigma weight residual 114.75 93.95 20.80 1.26e+00 6.30e-01 2.72e+02 angle pdb=" N ASP A 854 " pdb=" CA ASP A 854 " pdb=" CB ASP A 854 " ideal model delta sigma weight residual 111.15 127.08 -15.93 1.46e+00 4.69e-01 1.19e+02 angle pdb=" N ASP A 853 " pdb=" CA ASP A 853 " pdb=" C ASP A 853 " ideal model delta sigma weight residual 110.80 128.42 -17.62 2.13e+00 2.20e-01 6.84e+01 angle pdb=" CA GLN A 244 " pdb=" CB GLN A 244 " pdb=" CG GLN A 244 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CB MET A 998 " pdb=" CG MET A 998 " pdb=" SD MET A 998 " ideal model delta sigma weight residual 112.70 124.34 -11.64 3.00e+00 1.11e-01 1.51e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5780 17.85 - 35.71: 790 35.71 - 53.56: 226 53.56 - 71.42: 37 71.42 - 89.27: 16 Dihedral angle restraints: 6849 sinusoidal: 2750 harmonic: 4099 Sorted by residual: dihedral pdb=" CA PRO A 245 " pdb=" C PRO A 245 " pdb=" N ILE A 246 " pdb=" CA ILE A 246 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA MET B 458 " pdb=" C MET B 458 " pdb=" N ALA B 459 " pdb=" CA ALA B 459 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" N ASP A 854 " pdb=" C ASP A 854 " pdb=" CA ASP A 854 " pdb=" CB ASP A 854 " ideal model delta harmonic sigma weight residual 122.80 132.12 -9.32 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1702 0.105 - 0.210: 58 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ASP A 853 " pdb=" N ASP A 853 " pdb=" C ASP A 853 " pdb=" CB ASP A 853 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA PRO A 212 " pdb=" N PRO A 212 " pdb=" C PRO A 212 " pdb=" CB PRO A 212 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA PRO B 385 " pdb=" N PRO B 385 " pdb=" C PRO B 385 " pdb=" CB PRO B 385 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1761 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 384 " -0.073 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 385 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 43 " -0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO C 44 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 44 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 44 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 622 " 0.061 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO A 623 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.049 5.00e-02 4.00e+02 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 468 2.72 - 3.26: 10546 3.26 - 3.81: 16543 3.81 - 4.35: 19028 4.35 - 4.90: 34061 Nonbonded interactions: 80646 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" OE2 GLU A 459 " model vdw 2.171 3.040 nonbonded pdb=" O CYS A 725 " pdb=" NH1 ARG A 754 " model vdw 2.175 3.120 nonbonded pdb=" OE2 GLU B 550 " pdb=" OH TYR B 577 " model vdw 2.215 3.040 nonbonded pdb=" O SER A 726 " pdb=" OG SER A 726 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 351 " pdb=" OD2 ASP A 502 " model vdw 2.232 3.040 ... (remaining 80641 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 0.071 11313 Z= 0.179 Angle : 0.813 20.799 15322 Z= 0.440 Chirality : 0.047 0.525 1764 Planarity : 0.006 0.112 1939 Dihedral : 17.991 89.270 4177 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.32 % Allowed : 29.92 % Favored : 69.76 % 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: -0.70 (0.23), residues: 1395 helix: 1.85 (0.24), residues: 499 sheet: -1.03 (0.32), residues: 274 loop : -2.23 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 525 HIS 0.006 0.001 HIS B 492 PHE 0.022 0.002 PHE B 557 TYR 0.019 0.002 TYR A 856 ARG 0.006 0.001 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.19403 ( 423) hydrogen bonds : angle 6.17250 ( 1227) covalent geometry : bond 0.00391 (11313) covalent geometry : angle 0.81263 (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 157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 PHE cc_start: 0.7936 (m-10) cc_final: 0.7582 (m-80) REVERT: A 225 MET cc_start: 0.7895 (mtt) cc_final: 0.7607 (mtt) REVERT: A 415 LEU cc_start: 0.7397 (tt) cc_final: 0.6529 (mp) REVERT: A 499 MET cc_start: 0.7878 (mmt) cc_final: 0.7626 (mmt) REVERT: A 680 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7283 (mp0) REVERT: B 523 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8489 (mmtm) outliers start: 4 outliers final: 2 residues processed: 156 average time/residue: 0.2154 time to fit residues: 49.2775 Evaluate side-chains 139 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 854 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.165934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.128030 restraints weight = 13919.303| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.56 r_work: 0.3681 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11313 Z= 0.111 Angle : 0.593 8.430 15322 Z= 0.298 Chirality : 0.041 0.169 1764 Planarity : 0.005 0.063 1939 Dihedral : 4.392 44.513 1489 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.64 % Allowed : 26.08 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.23), residues: 1395 helix: 2.04 (0.24), residues: 512 sheet: -0.70 (0.32), residues: 281 loop : -2.06 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 525 HIS 0.003 0.001 HIS A 367 PHE 0.016 0.001 PHE A1005 TYR 0.014 0.001 TYR A 856 ARG 0.005 0.000 ARG B 174 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 423) hydrogen bonds : angle 4.33629 ( 1227) covalent geometry : bond 0.00243 (11313) covalent geometry : angle 0.59251 (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 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7573 (tmtt) REVERT: A 177 PHE cc_start: 0.7970 (m-10) cc_final: 0.7688 (m-80) REVERT: A 211 GLN cc_start: 0.6596 (mm-40) cc_final: 0.6073 (tp-100) REVERT: A 225 MET cc_start: 0.7951 (mtt) cc_final: 0.7562 (mtt) REVERT: A 254 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6751 (mp) REVERT: A 401 MET cc_start: 0.5717 (mtp) cc_final: 0.5431 (mtp) REVERT: A 717 CYS cc_start: 0.8193 (t) cc_final: 0.7661 (p) REVERT: A 847 ASN cc_start: 0.7516 (t0) cc_final: 0.7276 (t0) REVERT: A 1053 ASP cc_start: 0.7723 (p0) cc_final: 0.7402 (p0) REVERT: B 518 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7514 (t80) outliers start: 33 outliers final: 19 residues processed: 181 average time/residue: 0.2080 time to fit residues: 55.6479 Evaluate side-chains 158 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN C 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117410 restraints weight = 14872.204| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.51 r_work: 0.3573 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11313 Z= 0.224 Angle : 0.724 8.246 15322 Z= 0.370 Chirality : 0.046 0.176 1764 Planarity : 0.005 0.058 1939 Dihedral : 5.020 25.867 1485 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 6.40 % Allowed : 23.92 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.23), residues: 1395 helix: 1.55 (0.23), residues: 512 sheet: -0.99 (0.33), residues: 284 loop : -2.36 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 525 HIS 0.010 0.002 HIS B 492 PHE 0.022 0.002 PHE A 450 TYR 0.024 0.002 TYR A 856 ARG 0.004 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.05736 ( 423) hydrogen bonds : angle 4.64667 ( 1227) covalent geometry : bond 0.00534 (11313) covalent geometry : angle 0.72412 (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 209 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 129 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7046 (tpt) cc_final: 0.6815 (tpt) REVERT: A 211 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6278 (tp-100) REVERT: A 220 ASP cc_start: 0.8019 (t0) cc_final: 0.7796 (t0) REVERT: A 225 MET cc_start: 0.8284 (mtt) cc_final: 0.8012 (mtt) REVERT: A 401 MET cc_start: 0.6391 (mtp) cc_final: 0.6121 (mtp) REVERT: A 556 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 680 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7323 (mp0) REVERT: A 717 CYS cc_start: 0.8317 (t) cc_final: 0.7792 (p) REVERT: A 889 GLU cc_start: 0.8815 (tp30) cc_final: 0.8573 (tm-30) REVERT: A 910 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: A 1017 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6800 (mp) REVERT: C 49 MET cc_start: 0.6753 (ppp) cc_final: 0.6523 (ppp) REVERT: C 76 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6855 (pt) outliers start: 80 outliers final: 50 residues processed: 193 average time/residue: 0.2173 time to fit residues: 63.8928 Evaluate side-chains 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 0.0670 chunk 135 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.157591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121574 restraints weight = 14647.512| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.47 r_work: 0.3609 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11313 Z= 0.138 Angle : 0.620 9.797 15322 Z= 0.311 Chirality : 0.042 0.184 1764 Planarity : 0.004 0.058 1939 Dihedral : 4.596 25.408 1485 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.52 % Allowed : 25.52 % Favored : 68.96 % 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: -0.74 (0.23), residues: 1395 helix: 1.80 (0.24), residues: 517 sheet: -1.03 (0.33), residues: 274 loop : -2.37 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 525 HIS 0.006 0.001 HIS B 492 PHE 0.015 0.002 PHE A1005 TYR 0.017 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 423) hydrogen bonds : angle 4.28436 ( 1227) covalent geometry : bond 0.00323 (11313) covalent geometry : angle 0.61969 (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 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 131 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7425 (tpt) cc_final: 0.7174 (tpt) REVERT: A 192 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: A 211 GLN cc_start: 0.6626 (mm-40) cc_final: 0.5941 (tp-100) REVERT: A 214 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6666 (ptt-90) REVERT: A 220 ASP cc_start: 0.7816 (t0) cc_final: 0.7595 (t0) REVERT: A 224 ASP cc_start: 0.8569 (p0) cc_final: 0.8149 (p0) REVERT: A 225 MET cc_start: 0.8315 (mtt) cc_final: 0.7894 (mtp) REVERT: A 392 MET cc_start: 0.6167 (tmm) cc_final: 0.5464 (tmm) REVERT: A 401 MET cc_start: 0.6137 (mtp) cc_final: 0.5895 (mtp) REVERT: A 680 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7364 (mp0) REVERT: A 717 CYS cc_start: 0.8292 (t) cc_final: 0.7703 (p) REVERT: A 829 GLN cc_start: 0.8692 (tp40) cc_final: 0.8436 (tt0) REVERT: A 841 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9105 (mp) REVERT: A 1017 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6763 (mp) REVERT: B 518 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 49 MET cc_start: 0.6797 (ppp) cc_final: 0.6462 (ppp) outliers start: 69 outliers final: 45 residues processed: 190 average time/residue: 0.1874 time to fit residues: 53.8814 Evaluate side-chains 177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113610 restraints weight = 13630.135| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.79 r_work: 0.3533 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11313 Z= 0.108 Angle : 0.575 8.335 15322 Z= 0.288 Chirality : 0.041 0.195 1764 Planarity : 0.004 0.056 1939 Dihedral : 4.238 25.977 1485 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.32 % Allowed : 27.04 % Favored : 68.64 % 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: -0.50 (0.23), residues: 1395 helix: 2.07 (0.24), residues: 517 sheet: -0.94 (0.33), residues: 274 loop : -2.28 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 202 HIS 0.003 0.001 HIS A 814 PHE 0.012 0.001 PHE A1005 TYR 0.012 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 423) hydrogen bonds : angle 4.01374 ( 1227) covalent geometry : bond 0.00245 (11313) covalent geometry : angle 0.57469 (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 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7567 (tpt) cc_final: 0.7355 (tpt) REVERT: A 211 GLN cc_start: 0.6426 (mm-40) cc_final: 0.6058 (tp-100) REVERT: A 224 ASP cc_start: 0.8459 (p0) cc_final: 0.8016 (p0) REVERT: A 225 MET cc_start: 0.8228 (mtt) cc_final: 0.7858 (mtp) REVERT: A 392 MET cc_start: 0.5483 (tmm) cc_final: 0.4792 (tmm) REVERT: A 401 MET cc_start: 0.5174 (mtp) cc_final: 0.4855 (mtp) REVERT: A 427 ASN cc_start: 0.7905 (m110) cc_final: 0.7320 (p0) REVERT: A 556 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: A 680 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7271 (mp0) REVERT: A 829 GLN cc_start: 0.8559 (tp40) cc_final: 0.8327 (tt0) REVERT: A 1017 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6390 (mp) REVERT: A 1046 TRP cc_start: 0.8342 (t60) cc_final: 0.7772 (t60) REVERT: A 1053 ASP cc_start: 0.8006 (p0) cc_final: 0.7707 (p0) REVERT: B 518 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7606 (t80) REVERT: C 49 MET cc_start: 0.6507 (ppp) cc_final: 0.6150 (ppp) REVERT: C 76 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6579 (pt) outliers start: 54 outliers final: 39 residues processed: 183 average time/residue: 0.1902 time to fit residues: 52.6037 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114257 restraints weight = 13442.105| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.81 r_work: 0.3525 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11313 Z= 0.115 Angle : 0.597 14.973 15322 Z= 0.294 Chirality : 0.041 0.185 1764 Planarity : 0.004 0.056 1939 Dihedral : 4.225 25.464 1485 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.88 % Allowed : 26.48 % Favored : 68.64 % 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: -0.49 (0.23), residues: 1395 helix: 2.07 (0.24), residues: 517 sheet: -0.96 (0.33), residues: 274 loop : -2.26 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 202 HIS 0.004 0.001 HIS A 814 PHE 0.012 0.001 PHE B 278 TYR 0.010 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 423) hydrogen bonds : angle 3.95775 ( 1227) covalent geometry : bond 0.00267 (11313) covalent geometry : angle 0.59682 (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 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 211 GLN cc_start: 0.6570 (mm-40) cc_final: 0.5970 (tp-100) REVERT: A 214 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6689 (ptt-90) REVERT: A 224 ASP cc_start: 0.8413 (p0) cc_final: 0.7963 (p0) REVERT: A 225 MET cc_start: 0.8244 (mtt) cc_final: 0.7889 (mtp) REVERT: A 392 MET cc_start: 0.5479 (tmm) cc_final: 0.4682 (tmm) REVERT: A 401 MET cc_start: 0.5183 (mtp) cc_final: 0.4851 (mtp) REVERT: A 427 ASN cc_start: 0.7906 (m110) cc_final: 0.7387 (p0) REVERT: A 556 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 680 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7291 (mp0) REVERT: A 1017 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6302 (mp) REVERT: A 1053 ASP cc_start: 0.7936 (p0) cc_final: 0.7686 (p0) REVERT: B 172 ASP cc_start: 0.8341 (t0) cc_final: 0.7754 (p0) REVERT: B 330 ASP cc_start: 0.8245 (p0) cc_final: 0.7912 (p0) REVERT: B 518 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7628 (t80) REVERT: C 49 MET cc_start: 0.6368 (ppp) cc_final: 0.5952 (ppp) REVERT: C 76 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6680 (pt) outliers start: 61 outliers final: 48 residues processed: 181 average time/residue: 0.2054 time to fit residues: 57.4383 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 105 LEU 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: 5.9990 chunk 120 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.155939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118250 restraints weight = 14856.693| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.84 r_work: 0.3569 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11313 Z= 0.154 Angle : 0.628 13.758 15322 Z= 0.317 Chirality : 0.043 0.183 1764 Planarity : 0.004 0.057 1939 Dihedral : 4.518 25.505 1485 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.68 % Allowed : 26.24 % Favored : 68.08 % 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: -0.72 (0.23), residues: 1395 helix: 1.85 (0.24), residues: 516 sheet: -1.12 (0.33), residues: 278 loop : -2.33 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 202 HIS 0.006 0.001 HIS B 492 PHE 0.017 0.002 PHE A 450 TYR 0.011 0.001 TYR A 700 ARG 0.003 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 423) hydrogen bonds : angle 4.17459 ( 1227) covalent geometry : bond 0.00366 (11313) covalent geometry : angle 0.62836 (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 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 122 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.7841 (p-90) cc_final: 0.6925 (p90) REVERT: A 211 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6352 (tp-100) REVERT: A 224 ASP cc_start: 0.8644 (p0) cc_final: 0.8254 (p0) REVERT: A 225 MET cc_start: 0.8377 (mtt) cc_final: 0.7649 (mtp) REVERT: A 392 MET cc_start: 0.6164 (tmm) cc_final: 0.5438 (tmm) REVERT: A 401 MET cc_start: 0.6228 (mtp) cc_final: 0.5796 (mtp) REVERT: A 416 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7418 (ttmm) REVERT: A 427 ASN cc_start: 0.7870 (m110) cc_final: 0.7602 (p0) REVERT: A 556 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 680 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7457 (mp0) REVERT: A 1017 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6921 (mp) REVERT: A 1053 ASP cc_start: 0.8235 (p0) cc_final: 0.8028 (p0) REVERT: B 518 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7786 (t80) REVERT: C 49 MET cc_start: 0.6848 (ppp) cc_final: 0.6313 (ppp) REVERT: C 76 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7029 (pt) outliers start: 71 outliers final: 61 residues processed: 181 average time/residue: 0.1933 time to fit residues: 53.0326 Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 0.0000 chunk 68 optimal weight: 0.0020 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 30 optimal weight: 0.0980 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.162604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118274 restraints weight = 13410.279| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.91 r_work: 0.3556 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11313 Z= 0.093 Angle : 0.555 13.445 15322 Z= 0.273 Chirality : 0.040 0.188 1764 Planarity : 0.004 0.055 1939 Dihedral : 3.879 25.537 1485 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.60 % Allowed : 28.40 % Favored : 68.00 % 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: -0.33 (0.24), residues: 1395 helix: 2.18 (0.24), residues: 518 sheet: -0.79 (0.33), residues: 283 loop : -2.22 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 202 HIS 0.004 0.001 HIS A 367 PHE 0.021 0.001 PHE B 557 TYR 0.009 0.001 TYR A 856 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.02395 ( 423) hydrogen bonds : angle 3.74737 ( 1227) covalent geometry : bond 0.00202 (11313) covalent geometry : angle 0.55491 (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 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.7925 (p-90) cc_final: 0.6941 (p90) REVERT: A 211 GLN cc_start: 0.6430 (mm-40) cc_final: 0.5592 (tp-100) REVERT: A 214 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6058 (ptt-90) REVERT: A 224 ASP cc_start: 0.8374 (p0) cc_final: 0.7948 (p0) REVERT: A 225 MET cc_start: 0.8245 (mtt) cc_final: 0.7548 (mtp) REVERT: A 392 MET cc_start: 0.5277 (tmm) cc_final: 0.4585 (tmm) REVERT: A 401 MET cc_start: 0.4602 (mtp) cc_final: 0.4304 (mtp) REVERT: A 427 ASN cc_start: 0.8001 (m110) cc_final: 0.7555 (p0) REVERT: A 680 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7201 (mp0) REVERT: B 172 ASP cc_start: 0.8589 (t0) cc_final: 0.8118 (p0) REVERT: B 330 ASP cc_start: 0.8070 (p0) cc_final: 0.7718 (p0) REVERT: B 518 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7629 (t80) REVERT: C 49 MET cc_start: 0.6235 (ppp) cc_final: 0.5754 (ppp) outliers start: 45 outliers final: 31 residues processed: 174 average time/residue: 0.1903 time to fit residues: 50.4960 Evaluate side-chains 158 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.0050 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 9 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119079 restraints weight = 13316.042| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.77 r_work: 0.3581 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2979 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 : 0.559 13.064 15322 Z= 0.277 Chirality : 0.040 0.183 1764 Planarity : 0.004 0.054 1939 Dihedral : 3.821 25.319 1485 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.56 % Allowed : 29.68 % Favored : 67.76 % 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: -0.24 (0.24), residues: 1395 helix: 2.24 (0.24), residues: 518 sheet: -0.74 (0.33), residues: 277 loop : -2.15 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 202 HIS 0.003 0.001 HIS B 537 PHE 0.018 0.001 PHE B 557 TYR 0.006 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 423) hydrogen bonds : angle 3.67625 ( 1227) covalent geometry : bond 0.00217 (11313) covalent geometry : angle 0.55908 (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 164 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.7911 (p-90) cc_final: 0.6859 (p90) REVERT: A 211 GLN cc_start: 0.6605 (mm-40) cc_final: 0.6104 (tp40) REVERT: A 225 MET cc_start: 0.8214 (mtt) cc_final: 0.7868 (mtt) REVERT: A 392 MET cc_start: 0.5377 (tmm) cc_final: 0.4687 (tmm) REVERT: A 401 MET cc_start: 0.4824 (mtp) cc_final: 0.4502 (mtp) REVERT: A 427 ASN cc_start: 0.8066 (m110) cc_final: 0.7539 (p0) REVERT: A 680 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7243 (mp0) REVERT: B 172 ASP cc_start: 0.8510 (t0) cc_final: 0.8098 (p0) REVERT: B 330 ASP cc_start: 0.8032 (p0) cc_final: 0.7647 (p0) REVERT: C 49 MET cc_start: 0.6270 (ppp) cc_final: 0.5778 (ppp) outliers start: 32 outliers final: 29 residues processed: 157 average time/residue: 0.1962 time to fit residues: 47.2383 Evaluate side-chains 153 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116845 restraints weight = 13312.682| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.80 r_work: 0.3510 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11313 Z= 0.110 Angle : 0.582 12.839 15322 Z= 0.291 Chirality : 0.041 0.173 1764 Planarity : 0.004 0.055 1939 Dihedral : 3.931 23.700 1485 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.88 % Allowed : 29.36 % Favored : 67.76 % 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: -0.27 (0.23), residues: 1395 helix: 2.22 (0.24), residues: 518 sheet: -0.80 (0.33), residues: 282 loop : -2.15 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 202 HIS 0.003 0.001 HIS A 814 PHE 0.018 0.001 PHE B 557 TYR 0.017 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 423) hydrogen bonds : angle 3.76279 ( 1227) covalent geometry : bond 0.00253 (11313) covalent geometry : angle 0.58191 (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 162 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 211 GLN cc_start: 0.6612 (mm-40) cc_final: 0.6090 (tp40) REVERT: A 225 MET cc_start: 0.8125 (mtt) cc_final: 0.7738 (mtp) REVERT: A 234 MET cc_start: 0.7512 (ptp) cc_final: 0.7253 (ppp) REVERT: A 392 MET cc_start: 0.5343 (tmm) cc_final: 0.4659 (tmm) REVERT: A 401 MET cc_start: 0.4996 (mtp) cc_final: 0.4688 (mtp) REVERT: A 427 ASN cc_start: 0.8038 (m110) cc_final: 0.7515 (p0) REVERT: A 680 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7258 (mp0) REVERT: A 1017 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6320 (mp) REVERT: B 172 ASP cc_start: 0.8507 (t0) cc_final: 0.8087 (p0) REVERT: B 330 ASP cc_start: 0.8065 (p0) cc_final: 0.7688 (p0) REVERT: B 387 GLU cc_start: 0.8598 (mp0) cc_final: 0.8304 (pt0) REVERT: C 49 MET cc_start: 0.6288 (ppp) cc_final: 0.5790 (ppp) outliers start: 36 outliers final: 32 residues processed: 152 average time/residue: 0.2341 time to fit residues: 54.9416 Evaluate side-chains 157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.158995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.118886 restraints weight = 13498.807| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.95 r_work: 0.3537 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11313 Z= 0.099 Angle : 0.562 12.925 15322 Z= 0.279 Chirality : 0.040 0.172 1764 Planarity : 0.004 0.055 1939 Dihedral : 3.823 23.665 1485 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.80 % Allowed : 29.60 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.24), residues: 518 sheet: -0.72 (0.33), residues: 282 loop : -2.13 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 202 HIS 0.003 0.001 HIS A 814 PHE 0.018 0.001 PHE B 557 TYR 0.012 0.001 TYR A 856 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 423) hydrogen bonds : angle 3.69288 ( 1227) covalent geometry : bond 0.00227 (11313) covalent geometry : angle 0.56228 (15322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6339.54 seconds wall clock time: 111 minutes 16.39 seconds (6676.39 seconds total)