Starting phenix.real_space_refine on Wed Mar 4 02:38:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl7_32576/03_2026/7wl7_32576.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 42 5.16 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.08, per 1000 atoms: 0.20 Number of scatterers: 10198 At special positions: 0 Unit cell: (85.12, 127.68, 117.04, 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 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 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: 0.72 Conformation dependent library (CDL) restraints added in 523.2 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 66.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.502A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.901A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.839A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.055A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.567A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 161 " --> pdb=" O ASP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.964A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.920A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 Processing helix chain 'A' and resid 349 through 376 removed outlier: 3.741A pdb=" N HIS A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.531A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.581A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.527A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.814A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.569A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.651A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.605A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.930A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.654A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.718A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.720A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.588A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.931A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 105 removed outlier: 3.511A pdb=" N LEU B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.998A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.568A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.676A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.905A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.522A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.746A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.504A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.621A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 376 removed outlier: 3.621A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.623A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.548A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.694A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.843A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.576A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.504A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.618A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.622A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.673A pdb=" N VAL B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.643A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.756A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.717A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.674A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.473A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.497A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1683 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: 1.41 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 2251 1.46 - 1.58: 4873 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 1.98e+00 bond pdb=" C ILE A 296 " pdb=" O ILE A 296 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.70e-01 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.65e-01 bond pdb=" N ALA B 156 " pdb=" CA ALA B 156 " ideal model delta sigma weight residual 1.464 1.456 0.008 9.80e-03 1.04e+04 6.81e-01 bond pdb=" CA ILE A 208 " pdb=" CB ILE A 208 " ideal model delta sigma weight residual 1.533 1.542 -0.009 1.14e-02 7.69e+03 6.47e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13944 1.63 - 3.26: 155 3.26 - 4.89: 33 4.89 - 6.52: 2 6.52 - 8.15: 2 Bond angle restraints: 14136 Sorted by residual: angle pdb=" C ARG B 79 " pdb=" N VAL B 80 " pdb=" CA VAL B 80 " ideal model delta sigma weight residual 120.62 125.10 -4.48 1.64e+00 3.72e-01 7.47e+00 angle pdb=" C THR A 45 " pdb=" N LEU A 46 " pdb=" CA LEU A 46 " ideal model delta sigma weight residual 120.38 123.85 -3.47 1.37e+00 5.33e-01 6.41e+00 angle pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " pdb=" CG LEU B 162 " ideal model delta sigma weight residual 116.30 124.45 -8.15 3.50e+00 8.16e-02 5.42e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.25e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 114.08 -4.74 2.08e+00 2.31e-01 5.19e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5996 17.86 - 35.71: 142 35.71 - 53.57: 37 53.57 - 71.43: 2 71.43 - 89.29: 5 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 -84.19 84.19 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" N MET B 488 " pdb=" CA MET B 488 " pdb=" CB MET B 488 " pdb=" CG MET B 488 " ideal model delta sinusoidal sigma weight residual -60.00 -117.21 57.21 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET A 488 " pdb=" CA MET A 488 " pdb=" CB MET A 488 " pdb=" CG MET A 488 " ideal model delta sinusoidal sigma weight residual -60.00 -116.01 56.01 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1034 0.026 - 0.052: 404 0.052 - 0.078: 197 0.078 - 0.104: 65 0.104 - 0.130: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 112 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 553 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 300 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO A 301 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.016 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1346 2.75 - 3.29: 10806 3.29 - 3.83: 16661 3.83 - 4.36: 19574 4.36 - 4.90: 32910 Nonbonded interactions: 81297 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.223 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.248 3.120 ... (remaining 81292 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.002 0.020 10400 Z= 0.106 Angle : 0.495 8.151 14136 Z= 0.298 Chirality : 0.037 0.130 1718 Planarity : 0.003 0.034 1758 Dihedral : 8.843 89.286 3710 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 3.39 % Allowed : 5.26 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.19), residues: 1322 helix: -1.94 (0.14), residues: 820 sheet: -2.26 (0.88), residues: 34 loop : -3.08 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 512 TYR 0.007 0.001 TYR B 127 PHE 0.008 0.001 PHE B 555 TRP 0.003 0.000 TRP A 83 HIS 0.001 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00176 (10400) covalent geometry : angle 0.49539 (14136) hydrogen bonds : bond 0.22873 ( 575) hydrogen bonds : angle 6.63054 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 394 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7048 (tm) REVERT: A 97 VAL cc_start: 0.8846 (t) cc_final: 0.8519 (p) REVERT: A 122 PHE cc_start: 0.7965 (m-80) cc_final: 0.7566 (m-10) REVERT: A 145 SER cc_start: 0.8246 (m) cc_final: 0.7924 (p) REVERT: A 161 PHE cc_start: 0.7523 (m-80) cc_final: 0.6937 (m-80) REVERT: A 195 LEU cc_start: 0.8629 (tp) cc_final: 0.8237 (tp) REVERT: A 229 PHE cc_start: 0.8287 (t80) cc_final: 0.7890 (t80) REVERT: A 232 LEU cc_start: 0.9024 (tp) cc_final: 0.8762 (tp) REVERT: A 238 ILE cc_start: 0.8506 (mt) cc_final: 0.8218 (tp) REVERT: A 242 VAL cc_start: 0.8861 (m) cc_final: 0.8604 (p) REVERT: A 244 THR cc_start: 0.8293 (p) cc_final: 0.7846 (t) REVERT: A 276 LEU cc_start: 0.8150 (tp) cc_final: 0.7931 (tp) REVERT: A 361 TYR cc_start: 0.8669 (t80) cc_final: 0.8373 (t80) REVERT: A 385 PHE cc_start: 0.8179 (t80) cc_final: 0.7957 (t80) REVERT: A 394 PHE cc_start: 0.8151 (t80) cc_final: 0.6730 (t80) REVERT: A 398 PHE cc_start: 0.6568 (m-80) cc_final: 0.5904 (m-80) REVERT: A 432 MET cc_start: 0.7693 (tpt) cc_final: 0.7424 (tpt) REVERT: A 435 ILE cc_start: 0.8834 (mt) cc_final: 0.8581 (tp) REVERT: A 448 SER cc_start: 0.8546 (m) cc_final: 0.8093 (p) REVERT: A 470 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7523 (tpp80) REVERT: A 496 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 512 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: A 530 TYR cc_start: 0.7967 (m-80) cc_final: 0.7631 (m-10) REVERT: A 537 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7964 (ptpp) REVERT: A 543 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: A 549 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7376 (ttm-80) REVERT: A 578 TYR cc_start: 0.7429 (t80) cc_final: 0.6937 (t80) REVERT: A 580 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8610 (mmmt) REVERT: A 677 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7599 (ttm-80) REVERT: A 681 LYS cc_start: 0.8881 (tptt) cc_final: 0.8490 (tppt) REVERT: A 685 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8086 (mtm180) REVERT: A 687 ASP cc_start: 0.8179 (t0) cc_final: 0.7784 (t0) REVERT: A 694 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 698 ASP cc_start: 0.7678 (t0) cc_final: 0.7383 (t0) REVERT: A 701 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 704 GLU cc_start: 0.7734 (tt0) cc_final: 0.7449 (tt0) REVERT: A 732 GLN cc_start: 0.8231 (tt0) cc_final: 0.7518 (tm-30) REVERT: B 37 GLU cc_start: 0.7673 (pm20) cc_final: 0.7368 (pm20) REVERT: B 68 LEU cc_start: 0.8703 (tp) cc_final: 0.8386 (tp) REVERT: B 72 LEU cc_start: 0.8739 (mt) cc_final: 0.8527 (mp) REVERT: B 73 ASP cc_start: 0.7353 (t0) cc_final: 0.7099 (t0) REVERT: B 96 LEU cc_start: 0.8833 (mt) cc_final: 0.8563 (mm) REVERT: B 121 PHE cc_start: 0.7513 (t80) cc_final: 0.7186 (t80) REVERT: B 148 VAL cc_start: 0.9001 (t) cc_final: 0.8697 (p) REVERT: B 161 PHE cc_start: 0.7698 (m-80) cc_final: 0.7066 (m-80) REVERT: B 199 ILE cc_start: 0.9177 (mt) cc_final: 0.8942 (mt) REVERT: B 210 PHE cc_start: 0.7585 (p90) cc_final: 0.7297 (p90) REVERT: B 211 ILE cc_start: 0.8722 (tt) cc_final: 0.8322 (tp) REVERT: B 259 GLU cc_start: 0.7466 (tt0) cc_final: 0.4918 (tt0) REVERT: B 266 ASP cc_start: 0.7758 (m-30) cc_final: 0.7141 (p0) REVERT: B 271 ASP cc_start: 0.7617 (m-30) cc_final: 0.7371 (m-30) REVERT: B 276 LEU cc_start: 0.8228 (tp) cc_final: 0.8005 (tt) REVERT: B 287 GLU cc_start: 0.8222 (tp30) cc_final: 0.7249 (tp30) REVERT: B 288 LEU cc_start: 0.8770 (tp) cc_final: 0.8540 (tp) REVERT: B 293 LYS cc_start: 0.8243 (tppt) cc_final: 0.7749 (tppt) REVERT: B 304 VAL cc_start: 0.8733 (t) cc_final: 0.8451 (p) REVERT: B 355 SER cc_start: 0.8977 (m) cc_final: 0.8708 (p) REVERT: B 369 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7998 (mmmt) REVERT: B 371 TYR cc_start: 0.7449 (m-80) cc_final: 0.6906 (m-80) REVERT: B 384 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 426 ILE cc_start: 0.8834 (mt) cc_final: 0.8549 (tp) REVERT: B 432 MET cc_start: 0.7604 (tpt) cc_final: 0.7154 (tpt) REVERT: B 435 ILE cc_start: 0.8526 (mt) cc_final: 0.8320 (mm) REVERT: B 470 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7424 (tpp80) REVERT: B 473 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8377 (mppt) REVERT: B 475 ASN cc_start: 0.7120 (t0) cc_final: 0.6060 (t0) REVERT: B 478 ASP cc_start: 0.7240 (m-30) cc_final: 0.6551 (m-30) REVERT: B 486 CYS cc_start: 0.8601 (t) cc_final: 0.8371 (t) REVERT: B 492 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7564 (pp) REVERT: B 537 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8170 (ttmm) REVERT: B 549 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7422 (ttt90) REVERT: B 579 ASN cc_start: 0.8054 (m-40) cc_final: 0.7164 (m-40) REVERT: B 580 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8324 (mmmt) REVERT: B 668 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7047 (mt) REVERT: B 678 MET cc_start: 0.6961 (tpp) cc_final: 0.6606 (tpp) REVERT: B 681 LYS cc_start: 0.8901 (tptt) cc_final: 0.8559 (mmmt) REVERT: B 698 ASP cc_start: 0.7626 (t0) cc_final: 0.7272 (t0) REVERT: B 701 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 714 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7668 (ptp-110) REVERT: B 732 GLN cc_start: 0.7721 (tt0) cc_final: 0.7007 (tm-30) outliers start: 38 outliers final: 9 residues processed: 419 average time/residue: 0.1264 time to fit residues: 69.2571 Evaluate side-chains 360 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 345 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 207 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 421 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 730 GLN A 731 ASN B 135 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN B 730 GLN B 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096371 restraints weight = 23437.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099690 restraints weight = 11961.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101929 restraints weight = 7339.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103424 restraints weight = 5024.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104533 restraints weight = 3798.918| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10400 Z= 0.176 Angle : 0.669 11.134 14136 Z= 0.347 Chirality : 0.043 0.166 1718 Planarity : 0.005 0.037 1758 Dihedral : 6.266 83.152 1445 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.55 % Allowed : 12.21 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1322 helix: -0.17 (0.17), residues: 834 sheet: -3.03 (0.67), residues: 48 loop : -2.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.020 0.002 TYR A 377 PHE 0.023 0.002 PHE B 385 TRP 0.012 0.001 TRP B 83 HIS 0.010 0.002 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00359 (10400) covalent geometry : angle 0.66925 (14136) hydrogen bonds : bond 0.05090 ( 575) hydrogen bonds : angle 4.17722 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7291 (ttm110) cc_final: 0.7018 (ttm110) REVERT: A 46 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7068 (tm) REVERT: A 72 LEU cc_start: 0.9212 (mp) cc_final: 0.8869 (pp) REVERT: A 83 TRP cc_start: 0.6480 (m-10) cc_final: 0.6273 (m-10) REVERT: A 121 PHE cc_start: 0.8413 (t80) cc_final: 0.8101 (t80) REVERT: A 122 PHE cc_start: 0.8287 (m-80) cc_final: 0.7792 (m-10) REVERT: A 145 SER cc_start: 0.8605 (m) cc_final: 0.8146 (p) REVERT: A 160 HIS cc_start: 0.6973 (t-90) cc_final: 0.6440 (t-90) REVERT: A 161 PHE cc_start: 0.7579 (m-80) cc_final: 0.6505 (m-80) REVERT: A 182 ASP cc_start: 0.8358 (m-30) cc_final: 0.7987 (m-30) REVERT: A 213 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7531 (ptp-170) REVERT: A 229 PHE cc_start: 0.8575 (t80) cc_final: 0.8350 (t80) REVERT: A 235 GLN cc_start: 0.8219 (mm110) cc_final: 0.7901 (mm-40) REVERT: A 238 ILE cc_start: 0.8662 (mt) cc_final: 0.8350 (tp) REVERT: A 242 VAL cc_start: 0.9042 (m) cc_final: 0.8763 (p) REVERT: A 293 LYS cc_start: 0.8828 (tppt) cc_final: 0.8601 (tppt) REVERT: A 361 TYR cc_start: 0.8738 (t80) cc_final: 0.8504 (t80) REVERT: A 384 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 394 PHE cc_start: 0.8476 (t80) cc_final: 0.6937 (t80) REVERT: A 398 PHE cc_start: 0.6688 (m-80) cc_final: 0.5948 (m-80) REVERT: A 432 MET cc_start: 0.8077 (tpt) cc_final: 0.7634 (tpt) REVERT: A 435 ILE cc_start: 0.9114 (mt) cc_final: 0.8787 (tp) REVERT: A 459 LYS cc_start: 0.8965 (tppp) cc_final: 0.8551 (tppt) REVERT: A 470 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7413 (tpp80) REVERT: A 496 LEU cc_start: 0.8900 (mm) cc_final: 0.8563 (tp) REVERT: A 529 ILE cc_start: 0.8130 (tp) cc_final: 0.7798 (pt) REVERT: A 530 TYR cc_start: 0.8059 (m-80) cc_final: 0.7841 (m-10) REVERT: A 537 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8139 (mtpp) REVERT: A 556 TYR cc_start: 0.8718 (p90) cc_final: 0.8459 (p90) REVERT: A 576 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: A 578 TYR cc_start: 0.7524 (t80) cc_final: 0.7013 (t80) REVERT: A 580 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8652 (mmtm) REVERT: A 582 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8807 (mm) REVERT: A 677 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7654 (ttm-80) REVERT: A 678 MET cc_start: 0.7132 (tmm) cc_final: 0.5579 (tmm) REVERT: A 681 LYS cc_start: 0.9042 (tptt) cc_final: 0.8466 (mmmm) REVERT: A 685 ARG cc_start: 0.8621 (mtm180) cc_final: 0.8237 (mtm180) REVERT: A 687 ASP cc_start: 0.8463 (t0) cc_final: 0.8009 (t0) REVERT: A 698 ASP cc_start: 0.7663 (t0) cc_final: 0.7396 (t0) REVERT: A 701 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 704 GLU cc_start: 0.8115 (tt0) cc_final: 0.7709 (tt0) REVERT: A 714 ARG cc_start: 0.7920 (ptp90) cc_final: 0.7625 (mtt90) REVERT: A 732 GLN cc_start: 0.8539 (tt0) cc_final: 0.7628 (tm-30) REVERT: B 36 ARG cc_start: 0.8205 (tpp-160) cc_final: 0.7795 (mmt-90) REVERT: B 46 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7088 (tm) REVERT: B 68 LEU cc_start: 0.8904 (tp) cc_final: 0.8606 (tp) REVERT: B 73 ASP cc_start: 0.7878 (t0) cc_final: 0.7589 (t0) REVERT: B 96 LEU cc_start: 0.9097 (mt) cc_final: 0.8818 (mm) REVERT: B 121 PHE cc_start: 0.7778 (t80) cc_final: 0.7480 (t80) REVERT: B 161 PHE cc_start: 0.7838 (m-80) cc_final: 0.6968 (m-80) REVERT: B 199 ILE cc_start: 0.9184 (mt) cc_final: 0.8972 (mt) REVERT: B 203 PHE cc_start: 0.8405 (m-80) cc_final: 0.7625 (m-80) REVERT: B 211 ILE cc_start: 0.8644 (tt) cc_final: 0.7940 (pt) REVERT: B 235 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: B 264 ILE cc_start: 0.8645 (mm) cc_final: 0.8398 (mm) REVERT: B 271 ASP cc_start: 0.8076 (m-30) cc_final: 0.7868 (m-30) REVERT: B 273 ILE cc_start: 0.8706 (mt) cc_final: 0.8479 (pt) REVERT: B 276 LEU cc_start: 0.8699 (tp) cc_final: 0.8423 (tt) REVERT: B 282 CYS cc_start: 0.8611 (t) cc_final: 0.8376 (t) REVERT: B 287 GLU cc_start: 0.8557 (tp30) cc_final: 0.7665 (tp30) REVERT: B 288 LEU cc_start: 0.8960 (tp) cc_final: 0.8735 (tp) REVERT: B 292 PHE cc_start: 0.7415 (t80) cc_final: 0.7164 (t80) REVERT: B 293 LYS cc_start: 0.8121 (tppt) cc_final: 0.7657 (tppt) REVERT: B 304 VAL cc_start: 0.8685 (t) cc_final: 0.8440 (p) REVERT: B 355 SER cc_start: 0.9034 (m) cc_final: 0.8715 (p) REVERT: B 369 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8423 (mtmt) REVERT: B 383 GLN cc_start: 0.8350 (tp40) cc_final: 0.7838 (tp40) REVERT: B 384 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 421 GLN cc_start: 0.8228 (mm110) cc_final: 0.7944 (mm110) REVERT: B 426 ILE cc_start: 0.8797 (mt) cc_final: 0.8446 (tp) REVERT: B 432 MET cc_start: 0.8078 (tpt) cc_final: 0.7573 (tpt) REVERT: B 435 ILE cc_start: 0.8943 (mt) cc_final: 0.8638 (tp) REVERT: B 446 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: B 447 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8492 (mtpp) REVERT: B 470 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7359 (tpp80) REVERT: B 473 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8560 (mppt) REVERT: B 475 ASN cc_start: 0.7165 (t0) cc_final: 0.6800 (t0) REVERT: B 486 CYS cc_start: 0.9022 (t) cc_final: 0.8762 (t) REVERT: B 503 LEU cc_start: 0.8997 (mt) cc_final: 0.8783 (mm) REVERT: B 546 LYS cc_start: 0.8009 (tppt) cc_final: 0.7762 (tppt) REVERT: B 580 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8374 (mmmt) REVERT: B 677 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7681 (ttm-80) REVERT: B 678 MET cc_start: 0.7415 (tpp) cc_final: 0.6846 (tpp) REVERT: B 681 LYS cc_start: 0.9073 (tptt) cc_final: 0.8526 (mmmm) REVERT: B 697 ASP cc_start: 0.7881 (m-30) cc_final: 0.7664 (m-30) REVERT: B 698 ASP cc_start: 0.7955 (t0) cc_final: 0.7507 (t0) REVERT: B 701 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 714 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7530 (mtt90) REVERT: B 727 LEU cc_start: 0.8761 (mt) cc_final: 0.8200 (mt) REVERT: B 732 GLN cc_start: 0.8205 (tt0) cc_final: 0.7365 (tm-30) outliers start: 51 outliers final: 26 residues processed: 386 average time/residue: 0.1062 time to fit residues: 55.6435 Evaluate side-chains 377 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 346 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 731 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 289 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096746 restraints weight = 23382.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100143 restraints weight = 11973.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102265 restraints weight = 7282.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103742 restraints weight = 5036.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104818 restraints weight = 3840.177| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10400 Z= 0.140 Angle : 0.632 11.104 14136 Z= 0.322 Chirality : 0.042 0.173 1718 Planarity : 0.004 0.036 1758 Dihedral : 5.305 58.137 1434 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.65 % Allowed : 14.88 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1322 helix: 0.47 (0.18), residues: 836 sheet: -2.34 (0.86), residues: 36 loop : -2.35 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.016 0.001 TYR A 377 PHE 0.021 0.001 PHE A 354 TRP 0.021 0.001 TRP B 83 HIS 0.010 0.002 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00300 (10400) covalent geometry : angle 0.63241 (14136) hydrogen bonds : bond 0.04422 ( 575) hydrogen bonds : angle 3.99899 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.8195 (m-10) cc_final: 0.7962 (m-10) REVERT: A 46 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7078 (tm) REVERT: A 83 TRP cc_start: 0.6483 (m-10) cc_final: 0.6248 (m-10) REVERT: A 96 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 97 VAL cc_start: 0.9023 (t) cc_final: 0.8643 (p) REVERT: A 121 PHE cc_start: 0.8371 (t80) cc_final: 0.7982 (t80) REVERT: A 122 PHE cc_start: 0.8230 (m-80) cc_final: 0.7775 (m-10) REVERT: A 145 SER cc_start: 0.8683 (m) cc_final: 0.8211 (p) REVERT: A 160 HIS cc_start: 0.6892 (t-90) cc_final: 0.6376 (t-90) REVERT: A 161 PHE cc_start: 0.7586 (m-80) cc_final: 0.6676 (m-80) REVERT: A 182 ASP cc_start: 0.8348 (m-30) cc_final: 0.8007 (m-30) REVERT: A 229 PHE cc_start: 0.8585 (t80) cc_final: 0.8348 (t80) REVERT: A 235 GLN cc_start: 0.8154 (mm110) cc_final: 0.7936 (mm-40) REVERT: A 238 ILE cc_start: 0.8752 (mt) cc_final: 0.8481 (mt) REVERT: A 242 VAL cc_start: 0.9032 (m) cc_final: 0.8714 (p) REVERT: A 258 ILE cc_start: 0.8850 (mm) cc_final: 0.8509 (tp) REVERT: A 293 LYS cc_start: 0.8852 (tppt) cc_final: 0.8489 (tppt) REVERT: A 320 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7708 (pp20) REVERT: A 384 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 394 PHE cc_start: 0.8521 (t80) cc_final: 0.7730 (t80) REVERT: A 432 MET cc_start: 0.7972 (tpt) cc_final: 0.7527 (tpt) REVERT: A 435 ILE cc_start: 0.9076 (mt) cc_final: 0.8784 (tp) REVERT: A 470 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7403 (tpp80) REVERT: A 496 LEU cc_start: 0.8934 (mm) cc_final: 0.8576 (mm) REVERT: A 529 ILE cc_start: 0.8159 (tp) cc_final: 0.7867 (pt) REVERT: A 530 TYR cc_start: 0.8104 (m-80) cc_final: 0.7824 (m-80) REVERT: A 537 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7303 (mtpp) REVERT: A 543 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 556 TYR cc_start: 0.8714 (p90) cc_final: 0.8451 (p90) REVERT: A 578 TYR cc_start: 0.7474 (t80) cc_final: 0.6851 (t80) REVERT: A 580 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8646 (mmtm) REVERT: A 582 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 678 MET cc_start: 0.7279 (tmm) cc_final: 0.6625 (tmm) REVERT: A 681 LYS cc_start: 0.9042 (tptt) cc_final: 0.8508 (mmmm) REVERT: A 682 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 685 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8184 (mtm110) REVERT: A 687 ASP cc_start: 0.8435 (t0) cc_final: 0.7978 (t0) REVERT: A 694 LEU cc_start: 0.8748 (mm) cc_final: 0.8417 (mt) REVERT: A 701 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 704 GLU cc_start: 0.8114 (tt0) cc_final: 0.7690 (tt0) REVERT: A 714 ARG cc_start: 0.7859 (ptp90) cc_final: 0.7627 (mtt90) REVERT: A 732 GLN cc_start: 0.8464 (tt0) cc_final: 0.7554 (tm-30) REVERT: B 36 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7541 (mmt-90) REVERT: B 46 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7129 (tm) REVERT: B 68 LEU cc_start: 0.8915 (tp) cc_final: 0.8649 (tp) REVERT: B 73 ASP cc_start: 0.7936 (t0) cc_final: 0.7654 (t0) REVERT: B 130 PHE cc_start: 0.8162 (m-80) cc_final: 0.7789 (m-10) REVERT: B 161 PHE cc_start: 0.7769 (m-80) cc_final: 0.7172 (m-80) REVERT: B 182 ASP cc_start: 0.7848 (p0) cc_final: 0.7545 (p0) REVERT: B 199 ILE cc_start: 0.9175 (mt) cc_final: 0.8921 (mt) REVERT: B 203 PHE cc_start: 0.8421 (m-80) cc_final: 0.7650 (m-80) REVERT: B 211 ILE cc_start: 0.8593 (tt) cc_final: 0.7903 (pt) REVERT: B 262 GLN cc_start: 0.8320 (tp40) cc_final: 0.8119 (tp-100) REVERT: B 264 ILE cc_start: 0.8793 (mm) cc_final: 0.8511 (mm) REVERT: B 273 ILE cc_start: 0.8664 (mt) cc_final: 0.8436 (pt) REVERT: B 276 LEU cc_start: 0.8668 (tp) cc_final: 0.8395 (tt) REVERT: B 282 CYS cc_start: 0.8682 (t) cc_final: 0.8199 (t) REVERT: B 283 MET cc_start: 0.7931 (tpp) cc_final: 0.7185 (tpp) REVERT: B 286 LYS cc_start: 0.8939 (tppt) cc_final: 0.8520 (ptmm) REVERT: B 291 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7466 (ttp-110) REVERT: B 292 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7144 (t80) REVERT: B 293 LYS cc_start: 0.8086 (tppt) cc_final: 0.7572 (tppt) REVERT: B 355 SER cc_start: 0.8974 (m) cc_final: 0.8715 (p) REVERT: B 369 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8426 (mtmt) REVERT: B 374 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8428 (tmtt) REVERT: B 383 GLN cc_start: 0.8246 (tp40) cc_final: 0.7760 (tp40) REVERT: B 384 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7419 (mm-30) REVERT: B 413 GLN cc_start: 0.8051 (pt0) cc_final: 0.7423 (pp30) REVERT: B 426 ILE cc_start: 0.8818 (mt) cc_final: 0.8474 (tp) REVERT: B 432 MET cc_start: 0.8104 (tpt) cc_final: 0.7709 (tpt) REVERT: B 435 ILE cc_start: 0.8966 (mt) cc_final: 0.8728 (tp) REVERT: B 447 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8511 (mtpp) REVERT: B 470 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7383 (tpp80) REVERT: B 473 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8554 (mppt) REVERT: B 475 ASN cc_start: 0.7135 (t0) cc_final: 0.6713 (t0) REVERT: B 486 CYS cc_start: 0.8979 (t) cc_final: 0.8715 (t) REVERT: B 495 ASP cc_start: 0.8322 (p0) cc_final: 0.7991 (p0) REVERT: B 496 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 499 LEU cc_start: 0.8825 (tp) cc_final: 0.8590 (tp) REVERT: B 503 LEU cc_start: 0.8997 (mt) cc_final: 0.8716 (mp) REVERT: B 507 LEU cc_start: 0.8603 (tp) cc_final: 0.8346 (tt) REVERT: B 578 TYR cc_start: 0.7645 (t80) cc_final: 0.7399 (t80) REVERT: B 580 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8397 (mmtm) REVERT: B 668 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.6375 (tp) REVERT: B 677 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7680 (ttm-80) REVERT: B 678 MET cc_start: 0.7466 (tpp) cc_final: 0.6896 (tpp) REVERT: B 681 LYS cc_start: 0.9034 (tptt) cc_final: 0.8476 (mmmm) REVERT: B 698 ASP cc_start: 0.7942 (t0) cc_final: 0.7498 (t0) REVERT: B 701 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 705 GLN cc_start: 0.8536 (mt0) cc_final: 0.8317 (pp30) REVERT: B 714 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7502 (mtt90) REVERT: B 727 LEU cc_start: 0.8720 (mt) cc_final: 0.8382 (mt) REVERT: B 732 GLN cc_start: 0.8147 (tt0) cc_final: 0.7331 (tm-30) outliers start: 41 outliers final: 26 residues processed: 358 average time/residue: 0.1124 time to fit residues: 54.4495 Evaluate side-chains 357 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 703 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS A 457 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 246 ASN ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094401 restraints weight = 23418.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097573 restraints weight = 11887.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099740 restraints weight = 7302.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.101183 restraints weight = 4983.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102252 restraints weight = 3787.458| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10400 Z= 0.186 Angle : 0.638 10.314 14136 Z= 0.331 Chirality : 0.043 0.206 1718 Planarity : 0.004 0.043 1758 Dihedral : 5.333 58.662 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.17 % Allowed : 15.51 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1322 helix: 0.75 (0.18), residues: 848 sheet: -2.10 (0.88), residues: 36 loop : -2.30 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.016 0.002 TYR B 247 PHE 0.027 0.002 PHE A 484 TRP 0.023 0.001 TRP B 83 HIS 0.012 0.002 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00381 (10400) covalent geometry : angle 0.63783 (14136) hydrogen bonds : bond 0.04268 ( 575) hydrogen bonds : angle 3.92027 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.8447 (m-10) cc_final: 0.8217 (m-10) REVERT: A 66 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8121 (mmtt) REVERT: A 72 LEU cc_start: 0.9194 (mp) cc_final: 0.8961 (pp) REVERT: A 83 TRP cc_start: 0.6509 (m-10) cc_final: 0.6234 (m-10) REVERT: A 94 THR cc_start: 0.8521 (p) cc_final: 0.8075 (p) REVERT: A 96 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 97 VAL cc_start: 0.9118 (t) cc_final: 0.8791 (p) REVERT: A 122 PHE cc_start: 0.8247 (m-80) cc_final: 0.7758 (m-10) REVERT: A 134 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7706 (mtm-85) REVERT: A 145 SER cc_start: 0.8708 (m) cc_final: 0.8248 (p) REVERT: A 160 HIS cc_start: 0.7016 (t-90) cc_final: 0.6706 (t-90) REVERT: A 161 PHE cc_start: 0.7693 (m-80) cc_final: 0.7085 (m-80) REVERT: A 182 ASP cc_start: 0.8400 (m-30) cc_final: 0.8059 (m-30) REVERT: A 193 THR cc_start: 0.8793 (m) cc_final: 0.8398 (p) REVERT: A 200 GLN cc_start: 0.8381 (tt0) cc_final: 0.8023 (tt0) REVERT: A 229 PHE cc_start: 0.8590 (t80) cc_final: 0.8319 (t80) REVERT: A 235 GLN cc_start: 0.8149 (mm110) cc_final: 0.7918 (mm-40) REVERT: A 238 ILE cc_start: 0.8783 (mt) cc_final: 0.8497 (mt) REVERT: A 242 VAL cc_start: 0.9012 (m) cc_final: 0.8686 (p) REVERT: A 293 LYS cc_start: 0.8892 (tppt) cc_final: 0.8491 (tppt) REVERT: A 355 SER cc_start: 0.8843 (m) cc_final: 0.8597 (p) REVERT: A 361 TYR cc_start: 0.8708 (t80) cc_final: 0.8337 (t80) REVERT: A 384 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 385 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8614 (t80) REVERT: A 394 PHE cc_start: 0.8551 (t80) cc_final: 0.7766 (t80) REVERT: A 426 ILE cc_start: 0.8951 (mt) cc_final: 0.8483 (tt) REVERT: A 432 MET cc_start: 0.8029 (tpt) cc_final: 0.7585 (tpt) REVERT: A 435 ILE cc_start: 0.9127 (mt) cc_final: 0.8840 (tp) REVERT: A 470 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7543 (tpp80) REVERT: A 495 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7907 (p0) REVERT: A 496 LEU cc_start: 0.8990 (mm) cc_final: 0.8429 (mp) REVERT: A 529 ILE cc_start: 0.8247 (tp) cc_final: 0.7888 (pt) REVERT: A 530 TYR cc_start: 0.8121 (m-80) cc_final: 0.7786 (m-10) REVERT: A 531 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8004 (mmmm) REVERT: A 543 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 556 TYR cc_start: 0.8806 (p90) cc_final: 0.8525 (p90) REVERT: A 563 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8703 (tppp) REVERT: A 578 TYR cc_start: 0.7483 (t80) cc_final: 0.6966 (t80) REVERT: A 580 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8504 (mmtm) REVERT: A 582 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 583 LYS cc_start: 0.8950 (pptt) cc_final: 0.8674 (ptpt) REVERT: A 678 MET cc_start: 0.7385 (tmm) cc_final: 0.6969 (tmm) REVERT: A 681 LYS cc_start: 0.9076 (tptt) cc_final: 0.8550 (mmmm) REVERT: A 685 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8176 (mtm180) REVERT: A 687 ASP cc_start: 0.8418 (t0) cc_final: 0.8084 (t0) REVERT: A 694 LEU cc_start: 0.8820 (mm) cc_final: 0.8488 (mt) REVERT: A 701 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 704 GLU cc_start: 0.8119 (tt0) cc_final: 0.7655 (tt0) REVERT: A 714 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7625 (mtt90) REVERT: A 732 GLN cc_start: 0.8448 (tt0) cc_final: 0.7649 (tm-30) REVERT: B 36 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7774 (mmt-90) REVERT: B 46 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7156 (tm) REVERT: B 68 LEU cc_start: 0.8925 (tp) cc_final: 0.8663 (tp) REVERT: B 73 ASP cc_start: 0.7980 (t0) cc_final: 0.7665 (t0) REVERT: B 155 MET cc_start: 0.7773 (tpp) cc_final: 0.7570 (tpp) REVERT: B 160 HIS cc_start: 0.7186 (t-90) cc_final: 0.6631 (t-90) REVERT: B 161 PHE cc_start: 0.8012 (m-80) cc_final: 0.7397 (m-10) REVERT: B 203 PHE cc_start: 0.8398 (m-80) cc_final: 0.7773 (m-80) REVERT: B 211 ILE cc_start: 0.8679 (tt) cc_final: 0.8109 (pt) REVERT: B 213 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7324 (mtm-85) REVERT: B 262 GLN cc_start: 0.8446 (tp40) cc_final: 0.8213 (tp-100) REVERT: B 264 ILE cc_start: 0.8884 (mm) cc_final: 0.8650 (mm) REVERT: B 273 ILE cc_start: 0.8728 (mt) cc_final: 0.8509 (pt) REVERT: B 276 LEU cc_start: 0.8716 (tp) cc_final: 0.8458 (tt) REVERT: B 282 CYS cc_start: 0.8726 (t) cc_final: 0.8425 (t) REVERT: B 291 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7469 (ttp-110) REVERT: B 292 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6986 (t80) REVERT: B 293 LYS cc_start: 0.8202 (tppt) cc_final: 0.7695 (tppt) REVERT: B 355 SER cc_start: 0.8927 (m) cc_final: 0.8679 (p) REVERT: B 369 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8434 (mtmt) REVERT: B 383 GLN cc_start: 0.8300 (tp40) cc_final: 0.7900 (tp40) REVERT: B 384 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 413 GLN cc_start: 0.8084 (pt0) cc_final: 0.7513 (pp30) REVERT: B 421 GLN cc_start: 0.8222 (mm110) cc_final: 0.7962 (mm110) REVERT: B 426 ILE cc_start: 0.8861 (mt) cc_final: 0.8518 (tp) REVERT: B 432 MET cc_start: 0.8224 (tpt) cc_final: 0.7603 (tpt) REVERT: B 435 ILE cc_start: 0.9108 (mt) cc_final: 0.8837 (tp) REVERT: B 447 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8554 (mtpp) REVERT: B 470 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7465 (tpp80) REVERT: B 473 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8568 (mppt) REVERT: B 475 ASN cc_start: 0.7111 (t0) cc_final: 0.6743 (t0) REVERT: B 486 CYS cc_start: 0.8997 (t) cc_final: 0.8752 (t) REVERT: B 496 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 499 LEU cc_start: 0.8913 (tp) cc_final: 0.8650 (tp) REVERT: B 503 LEU cc_start: 0.9024 (mt) cc_final: 0.8746 (mp) REVERT: B 507 LEU cc_start: 0.8662 (tp) cc_final: 0.8391 (tt) REVERT: B 512 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8237 (mtm180) REVERT: B 531 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8475 (mmmm) REVERT: B 546 LYS cc_start: 0.8108 (tppt) cc_final: 0.7697 (tppt) REVERT: B 580 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8412 (mmtm) REVERT: B 677 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7699 (ttm-80) REVERT: B 681 LYS cc_start: 0.9091 (tptt) cc_final: 0.8536 (mmmm) REVERT: B 685 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8155 (mtm-85) REVERT: B 698 ASP cc_start: 0.8007 (t0) cc_final: 0.7561 (t70) REVERT: B 701 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 714 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7547 (mtt90) REVERT: B 728 HIS cc_start: 0.8930 (t-170) cc_final: 0.8324 (t-170) REVERT: B 732 GLN cc_start: 0.8156 (tt0) cc_final: 0.7619 (tm-30) outliers start: 58 outliers final: 37 residues processed: 364 average time/residue: 0.1100 time to fit residues: 54.3369 Evaluate side-chains 370 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 375 HIS ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 413 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093620 restraints weight = 23348.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096935 restraints weight = 11948.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099023 restraints weight = 7288.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100507 restraints weight = 5082.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101622 restraints weight = 3886.224| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10400 Z= 0.183 Angle : 0.666 10.656 14136 Z= 0.344 Chirality : 0.043 0.210 1718 Planarity : 0.004 0.043 1758 Dihedral : 5.254 53.156 1432 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.26 % Allowed : 17.29 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1322 helix: 0.91 (0.18), residues: 838 sheet: -2.04 (0.87), residues: 36 loop : -2.13 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.017 0.001 TYR B 377 PHE 0.020 0.001 PHE A 354 TRP 0.023 0.001 TRP B 83 HIS 0.020 0.003 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00383 (10400) covalent geometry : angle 0.66626 (14136) hydrogen bonds : bond 0.04177 ( 575) hydrogen bonds : angle 3.85662 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 337 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9163 (mp) cc_final: 0.8792 (pp) REVERT: A 83 TRP cc_start: 0.6548 (m-10) cc_final: 0.6265 (m-10) REVERT: A 96 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8914 (mm) REVERT: A 97 VAL cc_start: 0.9132 (t) cc_final: 0.8828 (p) REVERT: A 122 PHE cc_start: 0.8258 (m-80) cc_final: 0.7780 (m-10) REVERT: A 145 SER cc_start: 0.8682 (m) cc_final: 0.8252 (p) REVERT: A 160 HIS cc_start: 0.7040 (t-90) cc_final: 0.6686 (t-90) REVERT: A 161 PHE cc_start: 0.7831 (m-80) cc_final: 0.7354 (m-80) REVERT: A 182 ASP cc_start: 0.8390 (m-30) cc_final: 0.8057 (m-30) REVERT: A 235 GLN cc_start: 0.8134 (mm110) cc_final: 0.7849 (mm-40) REVERT: A 238 ILE cc_start: 0.8789 (mt) cc_final: 0.8507 (mt) REVERT: A 242 VAL cc_start: 0.9009 (m) cc_final: 0.8705 (p) REVERT: A 258 ILE cc_start: 0.8999 (tp) cc_final: 0.8608 (pt) REVERT: A 283 MET cc_start: 0.8142 (tpp) cc_final: 0.7293 (mpp) REVERT: A 286 LYS cc_start: 0.9105 (pttp) cc_final: 0.8748 (pttp) REVERT: A 293 LYS cc_start: 0.8897 (tppt) cc_final: 0.8517 (tppt) REVERT: A 355 SER cc_start: 0.8844 (m) cc_final: 0.8596 (p) REVERT: A 384 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 394 PHE cc_start: 0.8571 (t80) cc_final: 0.7768 (t80) REVERT: A 426 ILE cc_start: 0.8944 (mt) cc_final: 0.8494 (tt) REVERT: A 432 MET cc_start: 0.8038 (tpt) cc_final: 0.7619 (tpt) REVERT: A 435 ILE cc_start: 0.9145 (mt) cc_final: 0.8887 (tp) REVERT: A 470 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 488 MET cc_start: 0.8198 (tpp) cc_final: 0.7994 (tpp) REVERT: A 496 LEU cc_start: 0.9004 (mm) cc_final: 0.8593 (tp) REVERT: A 530 TYR cc_start: 0.8099 (m-80) cc_final: 0.7779 (m-80) REVERT: A 543 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 556 TYR cc_start: 0.8826 (p90) cc_final: 0.8598 (p90) REVERT: A 563 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8686 (tppp) REVERT: A 578 TYR cc_start: 0.7477 (t80) cc_final: 0.6780 (t80) REVERT: A 580 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8475 (mmmt) REVERT: A 582 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 678 MET cc_start: 0.7375 (tmm) cc_final: 0.7079 (tmm) REVERT: A 681 LYS cc_start: 0.9090 (tptt) cc_final: 0.8579 (mmmm) REVERT: A 682 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 685 ARG cc_start: 0.8531 (mtm180) cc_final: 0.8159 (mtm110) REVERT: A 687 ASP cc_start: 0.8453 (t0) cc_final: 0.8139 (t0) REVERT: A 694 LEU cc_start: 0.8809 (mm) cc_final: 0.8425 (mt) REVERT: A 701 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 704 GLU cc_start: 0.8116 (tt0) cc_final: 0.7633 (tt0) REVERT: A 714 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7673 (mtt90) REVERT: A 732 GLN cc_start: 0.8499 (tt0) cc_final: 0.7652 (tm-30) REVERT: B 20 TYR cc_start: 0.8131 (t80) cc_final: 0.7903 (t80) REVERT: B 36 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7721 (mmt-90) REVERT: B 46 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7144 (tm) REVERT: B 66 LYS cc_start: 0.8947 (tppt) cc_final: 0.8348 (tppt) REVERT: B 68 LEU cc_start: 0.8933 (tp) cc_final: 0.8661 (tp) REVERT: B 73 ASP cc_start: 0.7977 (t0) cc_final: 0.7738 (t0) REVERT: B 96 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 118 TYR cc_start: 0.8147 (m-10) cc_final: 0.7390 (m-80) REVERT: B 121 PHE cc_start: 0.7953 (t80) cc_final: 0.7737 (t80) REVERT: B 134 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7572 (mtm180) REVERT: B 160 HIS cc_start: 0.7202 (t-90) cc_final: 0.6909 (t-90) REVERT: B 182 ASP cc_start: 0.7861 (p0) cc_final: 0.7611 (p0) REVERT: B 203 PHE cc_start: 0.8390 (m-80) cc_final: 0.7836 (m-80) REVERT: B 211 ILE cc_start: 0.8674 (tt) cc_final: 0.8086 (pt) REVERT: B 213 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7680 (mtm-85) REVERT: B 240 LEU cc_start: 0.9257 (mt) cc_final: 0.8831 (tt) REVERT: B 262 GLN cc_start: 0.8419 (tp40) cc_final: 0.8181 (tm-30) REVERT: B 264 ILE cc_start: 0.8918 (mm) cc_final: 0.8670 (mm) REVERT: B 273 ILE cc_start: 0.8744 (mt) cc_final: 0.8520 (pt) REVERT: B 282 CYS cc_start: 0.8717 (t) cc_final: 0.8224 (t) REVERT: B 286 LYS cc_start: 0.8951 (tppt) cc_final: 0.8553 (ptmm) REVERT: B 287 GLU cc_start: 0.8535 (tp30) cc_final: 0.7726 (tp30) REVERT: B 292 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 293 LYS cc_start: 0.8243 (tppt) cc_final: 0.8031 (tptp) REVERT: B 355 SER cc_start: 0.8914 (m) cc_final: 0.8653 (p) REVERT: B 361 TYR cc_start: 0.8747 (t80) cc_final: 0.8528 (t80) REVERT: B 369 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8342 (mtmm) REVERT: B 383 GLN cc_start: 0.8295 (tp40) cc_final: 0.7973 (tp40) REVERT: B 384 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 413 GLN cc_start: 0.8047 (pt0) cc_final: 0.7596 (tm-30) REVERT: B 421 GLN cc_start: 0.8178 (mm110) cc_final: 0.7947 (mm110) REVERT: B 422 VAL cc_start: 0.8597 (t) cc_final: 0.8345 (m) REVERT: B 426 ILE cc_start: 0.8895 (mt) cc_final: 0.8533 (tp) REVERT: B 432 MET cc_start: 0.8123 (tpt) cc_final: 0.7606 (tpt) REVERT: B 435 ILE cc_start: 0.9116 (mt) cc_final: 0.8845 (tp) REVERT: B 447 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8583 (mtpp) REVERT: B 470 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7469 (tpp80) REVERT: B 473 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8579 (mppt) REVERT: B 475 ASN cc_start: 0.7125 (t0) cc_final: 0.6753 (t0) REVERT: B 486 CYS cc_start: 0.8959 (t) cc_final: 0.8696 (t) REVERT: B 495 ASP cc_start: 0.8362 (p0) cc_final: 0.8119 (p0) REVERT: B 496 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 499 LEU cc_start: 0.8928 (tp) cc_final: 0.8636 (tp) REVERT: B 503 LEU cc_start: 0.9019 (mt) cc_final: 0.8743 (mp) REVERT: B 512 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8258 (mtm180) REVERT: B 531 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8456 (mmmm) REVERT: B 556 TYR cc_start: 0.8817 (p90) cc_final: 0.8558 (p90) REVERT: B 563 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8702 (mmmm) REVERT: B 580 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8391 (mmtm) REVERT: B 587 ARG cc_start: 0.7009 (tpt170) cc_final: 0.6802 (tpt170) REVERT: B 677 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7743 (tpp80) REVERT: B 681 LYS cc_start: 0.9013 (tptt) cc_final: 0.8633 (tppt) REVERT: B 691 TYR cc_start: 0.7916 (m-10) cc_final: 0.7603 (m-10) REVERT: B 698 ASP cc_start: 0.8075 (t0) cc_final: 0.7557 (t70) REVERT: B 701 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 714 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7525 (mtt90) REVERT: B 728 HIS cc_start: 0.8697 (t-170) cc_final: 0.8491 (t-170) REVERT: B 732 GLN cc_start: 0.8437 (tt0) cc_final: 0.7529 (tm-30) outliers start: 59 outliers final: 44 residues processed: 365 average time/residue: 0.1106 time to fit residues: 54.6230 Evaluate side-chains 379 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095954 restraints weight = 23341.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099212 restraints weight = 11986.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101431 restraints weight = 7429.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102996 restraints weight = 5108.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103865 restraints weight = 3873.147| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10400 Z= 0.132 Angle : 0.669 12.283 14136 Z= 0.337 Chirality : 0.043 0.222 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.236 50.870 1432 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.72 % Allowed : 18.09 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1322 helix: 0.87 (0.18), residues: 840 sheet: -1.87 (0.87), residues: 36 loop : -1.99 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.030 0.002 TYR A 361 PHE 0.022 0.001 PHE A 354 TRP 0.016 0.001 TRP B 83 HIS 0.017 0.002 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00288 (10400) covalent geometry : angle 0.66867 (14136) hydrogen bonds : bond 0.04042 ( 575) hydrogen bonds : angle 3.81637 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9130 (mp) cc_final: 0.8751 (pp) REVERT: A 83 TRP cc_start: 0.6509 (m-10) cc_final: 0.6299 (m-10) REVERT: A 96 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 97 VAL cc_start: 0.9101 (t) cc_final: 0.8762 (p) REVERT: A 122 PHE cc_start: 0.8213 (m-80) cc_final: 0.7737 (m-10) REVERT: A 145 SER cc_start: 0.8634 (m) cc_final: 0.8179 (p) REVERT: A 160 HIS cc_start: 0.6970 (t-90) cc_final: 0.6691 (t-90) REVERT: A 161 PHE cc_start: 0.7738 (m-80) cc_final: 0.7259 (m-80) REVERT: A 182 ASP cc_start: 0.8299 (m-30) cc_final: 0.7988 (m-30) REVERT: A 235 GLN cc_start: 0.8054 (mm110) cc_final: 0.7784 (mm-40) REVERT: A 238 ILE cc_start: 0.8758 (mt) cc_final: 0.8480 (mt) REVERT: A 242 VAL cc_start: 0.9004 (m) cc_final: 0.8676 (p) REVERT: A 258 ILE cc_start: 0.8979 (tp) cc_final: 0.8593 (pt) REVERT: A 283 MET cc_start: 0.8113 (tpp) cc_final: 0.7778 (mpp) REVERT: A 286 LYS cc_start: 0.9044 (pttp) cc_final: 0.8756 (ptmt) REVERT: A 293 LYS cc_start: 0.8885 (tppt) cc_final: 0.8478 (tppt) REVERT: A 361 TYR cc_start: 0.8639 (t80) cc_final: 0.8372 (t80) REVERT: A 384 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 394 PHE cc_start: 0.8569 (t80) cc_final: 0.7773 (t80) REVERT: A 422 VAL cc_start: 0.8629 (t) cc_final: 0.8273 (m) REVERT: A 426 ILE cc_start: 0.8915 (mt) cc_final: 0.8482 (tt) REVERT: A 432 MET cc_start: 0.7961 (tpt) cc_final: 0.7500 (tpt) REVERT: A 435 ILE cc_start: 0.9104 (mt) cc_final: 0.8815 (tp) REVERT: A 464 GLN cc_start: 0.8627 (tt0) cc_final: 0.7799 (tp-100) REVERT: A 470 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7540 (tpp80) REVERT: A 488 MET cc_start: 0.8063 (tpp) cc_final: 0.7797 (tpp) REVERT: A 496 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 529 ILE cc_start: 0.8222 (tp) cc_final: 0.7837 (pt) REVERT: A 530 TYR cc_start: 0.8063 (m-80) cc_final: 0.7821 (m-10) REVERT: A 537 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7528 (ptpp) REVERT: A 543 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 556 TYR cc_start: 0.8753 (p90) cc_final: 0.8448 (p90) REVERT: A 563 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8675 (tppp) REVERT: A 578 TYR cc_start: 0.7434 (t80) cc_final: 0.6755 (t80) REVERT: A 579 ASN cc_start: 0.8301 (p0) cc_final: 0.7698 (p0) REVERT: A 580 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8602 (mmtm) REVERT: A 582 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 677 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7635 (ttm-80) REVERT: A 678 MET cc_start: 0.7364 (tmm) cc_final: 0.6998 (tmm) REVERT: A 681 LYS cc_start: 0.9077 (tptt) cc_final: 0.8528 (mmmm) REVERT: A 685 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8194 (mtm110) REVERT: A 687 ASP cc_start: 0.8432 (t0) cc_final: 0.8121 (t0) REVERT: A 694 LEU cc_start: 0.8719 (mm) cc_final: 0.8312 (mt) REVERT: A 698 ASP cc_start: 0.7617 (t0) cc_final: 0.7354 (t0) REVERT: A 701 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7988 (mm-30) REVERT: A 704 GLU cc_start: 0.8063 (tt0) cc_final: 0.7726 (tt0) REVERT: A 714 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7603 (mtt90) REVERT: A 732 GLN cc_start: 0.8441 (tt0) cc_final: 0.7758 (tm-30) REVERT: B 36 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7535 (mmt-90) REVERT: B 37 GLU cc_start: 0.8190 (pm20) cc_final: 0.7068 (pm20) REVERT: B 46 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7148 (tm) REVERT: B 66 LYS cc_start: 0.8981 (tppt) cc_final: 0.8647 (tppt) REVERT: B 68 LEU cc_start: 0.8907 (tp) cc_final: 0.8627 (tp) REVERT: B 73 ASP cc_start: 0.7952 (t0) cc_final: 0.7529 (t0) REVERT: B 161 PHE cc_start: 0.8011 (m-80) cc_final: 0.7783 (m-10) REVERT: B 188 LEU cc_start: 0.8770 (tp) cc_final: 0.8514 (tt) REVERT: B 193 THR cc_start: 0.8890 (m) cc_final: 0.8553 (p) REVERT: B 203 PHE cc_start: 0.8353 (m-80) cc_final: 0.7817 (m-80) REVERT: B 211 ILE cc_start: 0.8573 (tt) cc_final: 0.8068 (pt) REVERT: B 213 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7590 (mtm-85) REVERT: B 235 GLN cc_start: 0.8174 (mm110) cc_final: 0.7931 (mm-40) REVERT: B 240 LEU cc_start: 0.9233 (mt) cc_final: 0.8816 (tt) REVERT: B 264 ILE cc_start: 0.8832 (mm) cc_final: 0.8585 (mm) REVERT: B 273 ILE cc_start: 0.8708 (mt) cc_final: 0.8450 (pt) REVERT: B 282 CYS cc_start: 0.8730 (t) cc_final: 0.8207 (t) REVERT: B 286 LYS cc_start: 0.8927 (tppt) cc_final: 0.8531 (ptmm) REVERT: B 287 GLU cc_start: 0.8485 (tp30) cc_final: 0.7668 (tp30) REVERT: B 292 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6973 (t80) REVERT: B 355 SER cc_start: 0.8888 (m) cc_final: 0.8625 (p) REVERT: B 369 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8371 (mtmt) REVERT: B 371 TYR cc_start: 0.7539 (m-80) cc_final: 0.6847 (m-80) REVERT: B 375 HIS cc_start: 0.8664 (m170) cc_final: 0.8392 (m-70) REVERT: B 383 GLN cc_start: 0.8291 (tp40) cc_final: 0.7960 (tp40) REVERT: B 384 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 413 GLN cc_start: 0.7971 (pt0) cc_final: 0.7550 (tm-30) REVERT: B 426 ILE cc_start: 0.8855 (mt) cc_final: 0.8522 (tp) REVERT: B 432 MET cc_start: 0.8101 (tpt) cc_final: 0.7566 (tpt) REVERT: B 435 ILE cc_start: 0.9105 (mt) cc_final: 0.8845 (tp) REVERT: B 447 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8486 (mtpp) REVERT: B 470 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7427 (tpp80) REVERT: B 473 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8552 (mppt) REVERT: B 475 ASN cc_start: 0.7132 (t0) cc_final: 0.6776 (t0) REVERT: B 486 CYS cc_start: 0.8958 (t) cc_final: 0.8687 (t) REVERT: B 495 ASP cc_start: 0.8348 (p0) cc_final: 0.8090 (p0) REVERT: B 496 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8509 (mm) REVERT: B 499 LEU cc_start: 0.8900 (tp) cc_final: 0.8585 (tp) REVERT: B 503 LEU cc_start: 0.8980 (mt) cc_final: 0.8711 (mp) REVERT: B 507 LEU cc_start: 0.8589 (tp) cc_final: 0.8338 (tt) REVERT: B 512 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (mtm180) REVERT: B 546 LYS cc_start: 0.8104 (tppt) cc_final: 0.7592 (tppt) REVERT: B 576 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: B 580 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8355 (mmtm) REVERT: B 677 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7595 (ttm-80) REVERT: B 681 LYS cc_start: 0.8910 (tptt) cc_final: 0.8279 (tppp) REVERT: B 682 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 698 ASP cc_start: 0.8019 (t0) cc_final: 0.7524 (t70) REVERT: B 701 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 714 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7519 (mtt90) REVERT: B 728 HIS cc_start: 0.8744 (t-170) cc_final: 0.8392 (t-170) REVERT: B 732 GLN cc_start: 0.8402 (tt0) cc_final: 0.7483 (tm-30) outliers start: 53 outliers final: 38 residues processed: 360 average time/residue: 0.1094 time to fit residues: 53.3821 Evaluate side-chains 373 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS A 446 GLN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094426 restraints weight = 23275.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097687 restraints weight = 11844.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099807 restraints weight = 7222.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101353 restraints weight = 4987.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102220 restraints weight = 3796.176| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10400 Z= 0.181 Angle : 0.697 12.749 14136 Z= 0.355 Chirality : 0.044 0.211 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.145 51.713 1432 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.90 % Allowed : 18.98 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1322 helix: 0.98 (0.18), residues: 844 sheet: -1.80 (0.85), residues: 36 loop : -1.98 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 39 TYR 0.041 0.002 TYR A 361 PHE 0.033 0.002 PHE B 121 TRP 0.011 0.001 TRP B 83 HIS 0.018 0.002 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00385 (10400) covalent geometry : angle 0.69707 (14136) hydrogen bonds : bond 0.04104 ( 575) hydrogen bonds : angle 3.84680 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 344 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7447 (ttm110) cc_final: 0.7026 (mtp85) REVERT: A 72 LEU cc_start: 0.9163 (mp) cc_final: 0.8771 (pp) REVERT: A 83 TRP cc_start: 0.6517 (m-10) cc_final: 0.6257 (m-10) REVERT: A 96 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8854 (mm) REVERT: A 97 VAL cc_start: 0.9104 (t) cc_final: 0.8788 (p) REVERT: A 122 PHE cc_start: 0.8234 (m-80) cc_final: 0.7774 (m-10) REVERT: A 145 SER cc_start: 0.8613 (m) cc_final: 0.8206 (p) REVERT: A 160 HIS cc_start: 0.7037 (t-90) cc_final: 0.6761 (t-90) REVERT: A 161 PHE cc_start: 0.7808 (m-80) cc_final: 0.7441 (m-80) REVERT: A 182 ASP cc_start: 0.8335 (m-30) cc_final: 0.7777 (m-30) REVERT: A 200 GLN cc_start: 0.8347 (tt0) cc_final: 0.7979 (tt0) REVERT: A 213 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7486 (ptp-170) REVERT: A 235 GLN cc_start: 0.8108 (mm110) cc_final: 0.7882 (mm-40) REVERT: A 238 ILE cc_start: 0.8784 (mt) cc_final: 0.8514 (mt) REVERT: A 242 VAL cc_start: 0.9014 (m) cc_final: 0.8701 (p) REVERT: A 286 LYS cc_start: 0.9071 (pttp) cc_final: 0.8650 (pttp) REVERT: A 293 LYS cc_start: 0.8881 (tppt) cc_final: 0.8472 (tppt) REVERT: A 361 TYR cc_start: 0.8726 (t80) cc_final: 0.8471 (t80) REVERT: A 384 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 394 PHE cc_start: 0.8593 (t80) cc_final: 0.7820 (t80) REVERT: A 426 ILE cc_start: 0.8966 (mt) cc_final: 0.8501 (tt) REVERT: A 432 MET cc_start: 0.8014 (tpt) cc_final: 0.7565 (tpt) REVERT: A 435 ILE cc_start: 0.9123 (mt) cc_final: 0.8849 (tp) REVERT: A 470 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7596 (tpp80) REVERT: A 496 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 529 ILE cc_start: 0.8254 (tp) cc_final: 0.7920 (pt) REVERT: A 530 TYR cc_start: 0.8113 (m-80) cc_final: 0.7829 (m-10) REVERT: A 543 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 556 TYR cc_start: 0.8797 (p90) cc_final: 0.8519 (p90) REVERT: A 563 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8682 (tppp) REVERT: A 578 TYR cc_start: 0.7495 (t80) cc_final: 0.6609 (t80) REVERT: A 579 ASN cc_start: 0.8310 (p0) cc_final: 0.7718 (p0) REVERT: A 580 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8607 (mmtm) REVERT: A 582 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 677 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7641 (ttm-80) REVERT: A 678 MET cc_start: 0.7389 (tmm) cc_final: 0.7121 (tmm) REVERT: A 681 LYS cc_start: 0.9096 (tptt) cc_final: 0.8579 (mmmm) REVERT: A 682 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 685 ARG cc_start: 0.8491 (mtm180) cc_final: 0.8198 (mtm110) REVERT: A 687 ASP cc_start: 0.8448 (t0) cc_final: 0.8121 (t0) REVERT: A 694 LEU cc_start: 0.8794 (mm) cc_final: 0.8393 (mt) REVERT: A 698 ASP cc_start: 0.7649 (t0) cc_final: 0.7426 (t0) REVERT: A 701 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8008 (mm-30) REVERT: A 704 GLU cc_start: 0.8096 (tt0) cc_final: 0.7730 (tt0) REVERT: A 714 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7628 (mtt90) REVERT: A 732 GLN cc_start: 0.8515 (tt0) cc_final: 0.7674 (tm-30) REVERT: B 36 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7865 (mmt-90) REVERT: B 39 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7054 (mtp85) REVERT: B 46 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7142 (tm) REVERT: B 66 LYS cc_start: 0.8964 (tppt) cc_final: 0.8637 (tppt) REVERT: B 68 LEU cc_start: 0.8936 (tp) cc_final: 0.8646 (tp) REVERT: B 73 ASP cc_start: 0.7997 (t0) cc_final: 0.7413 (t0) REVERT: B 118 TYR cc_start: 0.8168 (m-10) cc_final: 0.7395 (m-80) REVERT: B 134 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.7321 (ptp-170) REVERT: B 193 THR cc_start: 0.8901 (m) cc_final: 0.8557 (p) REVERT: B 203 PHE cc_start: 0.8344 (m-80) cc_final: 0.7842 (m-80) REVERT: B 211 ILE cc_start: 0.8637 (tt) cc_final: 0.8109 (pt) REVERT: B 213 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7501 (mtm-85) REVERT: B 264 ILE cc_start: 0.8912 (mm) cc_final: 0.8646 (mm) REVERT: B 273 ILE cc_start: 0.8740 (mt) cc_final: 0.8512 (pt) REVERT: B 282 CYS cc_start: 0.8749 (t) cc_final: 0.8454 (t) REVERT: B 287 GLU cc_start: 0.8478 (tp30) cc_final: 0.7626 (tp30) REVERT: B 292 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 355 SER cc_start: 0.8883 (m) cc_final: 0.8620 (p) REVERT: B 361 TYR cc_start: 0.8755 (t80) cc_final: 0.8525 (t80) REVERT: B 369 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8392 (mtmt) REVERT: B 371 TYR cc_start: 0.7547 (m-80) cc_final: 0.6939 (m-80) REVERT: B 383 GLN cc_start: 0.8302 (tp40) cc_final: 0.7967 (tp40) REVERT: B 384 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 413 GLN cc_start: 0.8013 (pt0) cc_final: 0.7560 (tm-30) REVERT: B 421 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8072 (mm110) REVERT: B 422 VAL cc_start: 0.8584 (t) cc_final: 0.8331 (m) REVERT: B 426 ILE cc_start: 0.8909 (mt) cc_final: 0.8537 (tp) REVERT: B 432 MET cc_start: 0.8140 (tpt) cc_final: 0.7652 (tpt) REVERT: B 435 ILE cc_start: 0.9131 (mt) cc_final: 0.8853 (tp) REVERT: B 447 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8515 (mtpp) REVERT: B 470 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7467 (tpp80) REVERT: B 473 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8568 (mppt) REVERT: B 475 ASN cc_start: 0.7143 (t0) cc_final: 0.6802 (t0) REVERT: B 486 CYS cc_start: 0.8942 (t) cc_final: 0.8669 (t) REVERT: B 495 ASP cc_start: 0.8390 (p0) cc_final: 0.8069 (p0) REVERT: B 496 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8529 (mm) REVERT: B 499 LEU cc_start: 0.8938 (tp) cc_final: 0.8628 (tp) REVERT: B 503 LEU cc_start: 0.9033 (mt) cc_final: 0.8764 (mp) REVERT: B 507 LEU cc_start: 0.8656 (tp) cc_final: 0.8409 (tt) REVERT: B 512 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8239 (mtm180) REVERT: B 556 TYR cc_start: 0.8786 (p90) cc_final: 0.8530 (p90) REVERT: B 576 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7570 (mtm-85) REVERT: B 580 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8354 (mmtm) REVERT: B 668 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7583 (tp) REVERT: B 677 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7602 (ttm-80) REVERT: B 681 LYS cc_start: 0.8880 (tptt) cc_final: 0.8290 (tppp) REVERT: B 682 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 691 TYR cc_start: 0.7895 (m-10) cc_final: 0.7565 (m-10) REVERT: B 697 ASP cc_start: 0.8015 (m-30) cc_final: 0.7766 (m-30) REVERT: B 698 ASP cc_start: 0.8021 (t0) cc_final: 0.7493 (t70) REVERT: B 701 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 714 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7603 (mtt90) REVERT: B 724 ASP cc_start: 0.8264 (t0) cc_final: 0.8052 (t0) REVERT: B 728 HIS cc_start: 0.8846 (t-170) cc_final: 0.8455 (t-170) REVERT: B 732 GLN cc_start: 0.8498 (tt0) cc_final: 0.7640 (tm-30) outliers start: 55 outliers final: 41 residues processed: 368 average time/residue: 0.1151 time to fit residues: 57.1923 Evaluate side-chains 390 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 341 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 110 optimal weight: 0.0170 chunk 93 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094338 restraints weight = 23314.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097596 restraints weight = 11851.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099809 restraints weight = 7275.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101348 restraints weight = 4985.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102251 restraints weight = 3776.817| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10400 Z= 0.149 Angle : 0.705 15.680 14136 Z= 0.356 Chirality : 0.043 0.182 1718 Planarity : 0.004 0.040 1758 Dihedral : 5.170 51.057 1430 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.17 % Allowed : 19.79 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.24), residues: 1322 helix: 0.99 (0.18), residues: 828 sheet: -1.68 (0.86), residues: 36 loop : -1.98 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.044 0.002 TYR B 105 PHE 0.023 0.001 PHE A 354 TRP 0.011 0.001 TRP B 83 HIS 0.019 0.002 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00332 (10400) covalent geometry : angle 0.70467 (14136) hydrogen bonds : bond 0.04093 ( 575) hydrogen bonds : angle 3.90669 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9147 (mp) cc_final: 0.8741 (pp) REVERT: A 83 TRP cc_start: 0.6560 (m-10) cc_final: 0.6317 (m-10) REVERT: A 96 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8836 (mm) REVERT: A 97 VAL cc_start: 0.9080 (t) cc_final: 0.8759 (p) REVERT: A 122 PHE cc_start: 0.8226 (m-80) cc_final: 0.7737 (m-10) REVERT: A 145 SER cc_start: 0.8637 (m) cc_final: 0.8208 (p) REVERT: A 160 HIS cc_start: 0.7061 (t-90) cc_final: 0.6772 (t-90) REVERT: A 161 PHE cc_start: 0.7799 (m-80) cc_final: 0.7390 (m-80) REVERT: A 193 THR cc_start: 0.8697 (m) cc_final: 0.8426 (p) REVERT: A 200 GLN cc_start: 0.8345 (tt0) cc_final: 0.7973 (tt0) REVERT: A 235 GLN cc_start: 0.8068 (mm110) cc_final: 0.7834 (mm-40) REVERT: A 238 ILE cc_start: 0.8773 (mt) cc_final: 0.8494 (mt) REVERT: A 286 LYS cc_start: 0.9048 (pttp) cc_final: 0.8673 (ptmt) REVERT: A 293 LYS cc_start: 0.8889 (tppt) cc_final: 0.8471 (tppt) REVERT: A 349 MET cc_start: 0.6680 (ptm) cc_final: 0.6466 (ptm) REVERT: A 361 TYR cc_start: 0.8713 (t80) cc_final: 0.8486 (t80) REVERT: A 384 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 394 PHE cc_start: 0.8592 (t80) cc_final: 0.7781 (t80) REVERT: A 426 ILE cc_start: 0.8959 (mt) cc_final: 0.8487 (tt) REVERT: A 432 MET cc_start: 0.8002 (tpt) cc_final: 0.7524 (tpt) REVERT: A 435 ILE cc_start: 0.9120 (mt) cc_final: 0.8846 (tp) REVERT: A 459 LYS cc_start: 0.9051 (tppp) cc_final: 0.8506 (tppt) REVERT: A 464 GLN cc_start: 0.8523 (tt0) cc_final: 0.7964 (tp40) REVERT: A 470 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7573 (tpp80) REVERT: A 488 MET cc_start: 0.8131 (tpp) cc_final: 0.7853 (tpp) REVERT: A 496 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 514 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 529 ILE cc_start: 0.8273 (tp) cc_final: 0.7923 (pt) REVERT: A 543 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 556 TYR cc_start: 0.8794 (p90) cc_final: 0.8480 (p90) REVERT: A 563 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8700 (tppp) REVERT: A 578 TYR cc_start: 0.7561 (t80) cc_final: 0.6894 (t80) REVERT: A 579 ASN cc_start: 0.8284 (p0) cc_final: 0.7983 (p0) REVERT: A 580 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8575 (mmmt) REVERT: A 582 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 677 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7636 (ttm-80) REVERT: A 678 MET cc_start: 0.7369 (tmm) cc_final: 0.7012 (tmm) REVERT: A 681 LYS cc_start: 0.9094 (tptt) cc_final: 0.8568 (mmmm) REVERT: A 685 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8180 (mtm180) REVERT: A 687 ASP cc_start: 0.8445 (t0) cc_final: 0.8114 (t0) REVERT: A 694 LEU cc_start: 0.8770 (mm) cc_final: 0.8331 (mt) REVERT: A 698 ASP cc_start: 0.7649 (t0) cc_final: 0.7389 (t0) REVERT: A 701 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 704 GLU cc_start: 0.8084 (tt0) cc_final: 0.7742 (tt0) REVERT: A 714 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7620 (mtt90) REVERT: A 732 GLN cc_start: 0.8510 (tt0) cc_final: 0.7669 (tm-30) REVERT: B 36 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7778 (mmt-90) REVERT: B 39 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7102 (mtp85) REVERT: B 46 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7136 (tm) REVERT: B 66 LYS cc_start: 0.8948 (tppt) cc_final: 0.8588 (tppt) REVERT: B 68 LEU cc_start: 0.8944 (tp) cc_final: 0.8655 (tp) REVERT: B 73 ASP cc_start: 0.7908 (t0) cc_final: 0.7517 (t0) REVERT: B 105 TYR cc_start: 0.8724 (m-80) cc_final: 0.8267 (m-80) REVERT: B 118 TYR cc_start: 0.8141 (m-10) cc_final: 0.7365 (m-80) REVERT: B 134 ARG cc_start: 0.7658 (ptp-110) cc_final: 0.7331 (ptp-170) REVERT: B 182 ASP cc_start: 0.7897 (p0) cc_final: 0.7631 (p0) REVERT: B 193 THR cc_start: 0.8799 (m) cc_final: 0.8444 (p) REVERT: B 203 PHE cc_start: 0.8318 (m-80) cc_final: 0.7769 (m-80) REVERT: B 211 ILE cc_start: 0.8551 (tt) cc_final: 0.8017 (pt) REVERT: B 213 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7475 (mtm-85) REVERT: B 240 LEU cc_start: 0.9250 (mt) cc_final: 0.8775 (tt) REVERT: B 262 GLN cc_start: 0.8430 (tp40) cc_final: 0.8146 (tp-100) REVERT: B 264 ILE cc_start: 0.8902 (mm) cc_final: 0.8646 (mm) REVERT: B 273 ILE cc_start: 0.8735 (mt) cc_final: 0.8487 (pt) REVERT: B 282 CYS cc_start: 0.8719 (t) cc_final: 0.8423 (t) REVERT: B 287 GLU cc_start: 0.8448 (tp30) cc_final: 0.7586 (tp30) REVERT: B 292 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 355 SER cc_start: 0.8864 (m) cc_final: 0.8587 (p) REVERT: B 361 TYR cc_start: 0.8756 (t80) cc_final: 0.8497 (t80) REVERT: B 369 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8378 (mtmt) REVERT: B 371 TYR cc_start: 0.7432 (m-80) cc_final: 0.6931 (m-80) REVERT: B 383 GLN cc_start: 0.8271 (tp40) cc_final: 0.7895 (tp40) REVERT: B 384 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7348 (mm-30) REVERT: B 413 GLN cc_start: 0.7955 (pt0) cc_final: 0.7531 (tm-30) REVERT: B 421 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7997 (mm110) REVERT: B 422 VAL cc_start: 0.8549 (t) cc_final: 0.8301 (m) REVERT: B 426 ILE cc_start: 0.8881 (mt) cc_final: 0.8541 (tp) REVERT: B 432 MET cc_start: 0.8085 (tpt) cc_final: 0.7591 (tpt) REVERT: B 435 ILE cc_start: 0.9128 (mt) cc_final: 0.8854 (tp) REVERT: B 447 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8464 (mtpp) REVERT: B 470 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7440 (tpp80) REVERT: B 473 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8543 (mppt) REVERT: B 475 ASN cc_start: 0.7147 (t0) cc_final: 0.6785 (t0) REVERT: B 486 CYS cc_start: 0.8894 (t) cc_final: 0.8650 (t) REVERT: B 495 ASP cc_start: 0.8351 (p0) cc_final: 0.8122 (p0) REVERT: B 496 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 499 LEU cc_start: 0.8920 (tp) cc_final: 0.8616 (tp) REVERT: B 503 LEU cc_start: 0.9050 (mt) cc_final: 0.8794 (mp) REVERT: B 507 LEU cc_start: 0.8620 (tp) cc_final: 0.8370 (tt) REVERT: B 512 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8220 (mtm180) REVERT: B 514 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 537 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8370 (mmtp) REVERT: B 546 LYS cc_start: 0.8095 (tppt) cc_final: 0.7596 (tppt) REVERT: B 556 TYR cc_start: 0.8737 (p90) cc_final: 0.8537 (p90) REVERT: B 576 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: B 580 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8339 (mmtm) REVERT: B 668 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7495 (tp) REVERT: B 677 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7625 (ttm-80) REVERT: B 681 LYS cc_start: 0.8864 (tptt) cc_final: 0.8238 (tppp) REVERT: B 682 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 691 TYR cc_start: 0.7849 (m-10) cc_final: 0.7551 (m-10) REVERT: B 698 ASP cc_start: 0.8020 (t0) cc_final: 0.7496 (t70) REVERT: B 701 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 714 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7600 (mtt90) REVERT: B 724 ASP cc_start: 0.8188 (t0) cc_final: 0.7940 (t0) REVERT: B 728 HIS cc_start: 0.8830 (t-170) cc_final: 0.8430 (t-170) REVERT: B 732 GLN cc_start: 0.8450 (tt0) cc_final: 0.7655 (tm-30) outliers start: 58 outliers final: 43 residues processed: 376 average time/residue: 0.1095 time to fit residues: 55.8628 Evaluate side-chains 392 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.112392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094677 restraints weight = 23272.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097994 restraints weight = 11908.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100151 restraints weight = 7286.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101731 restraints weight = 5036.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102609 restraints weight = 3823.229| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10400 Z= 0.161 Angle : 0.716 14.549 14136 Z= 0.363 Chirality : 0.044 0.172 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.207 51.228 1430 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.35 % Allowed : 20.23 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1322 helix: 1.02 (0.18), residues: 830 sheet: -1.48 (0.88), residues: 36 loop : -1.98 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 685 TYR 0.041 0.002 TYR B 105 PHE 0.025 0.002 PHE B 394 TRP 0.010 0.001 TRP B 83 HIS 0.012 0.002 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00358 (10400) covalent geometry : angle 0.71571 (14136) hydrogen bonds : bond 0.04095 ( 575) hydrogen bonds : angle 3.91223 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 348 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9151 (mp) cc_final: 0.8743 (pp) REVERT: A 83 TRP cc_start: 0.6580 (m-10) cc_final: 0.6328 (m-10) REVERT: A 96 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 97 VAL cc_start: 0.9089 (t) cc_final: 0.8766 (p) REVERT: A 122 PHE cc_start: 0.8229 (m-80) cc_final: 0.7764 (m-10) REVERT: A 134 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7548 (mtm-85) REVERT: A 145 SER cc_start: 0.8626 (m) cc_final: 0.8206 (p) REVERT: A 160 HIS cc_start: 0.7048 (t-90) cc_final: 0.6728 (t-90) REVERT: A 161 PHE cc_start: 0.7680 (m-80) cc_final: 0.7150 (m-80) REVERT: A 193 THR cc_start: 0.8702 (m) cc_final: 0.8426 (p) REVERT: A 235 GLN cc_start: 0.8085 (mm110) cc_final: 0.7874 (mm-40) REVERT: A 238 ILE cc_start: 0.8777 (mt) cc_final: 0.8506 (mt) REVERT: A 283 MET cc_start: 0.7968 (tpp) cc_final: 0.7419 (mpp) REVERT: A 286 LYS cc_start: 0.9051 (pttp) cc_final: 0.8763 (ptmt) REVERT: A 293 LYS cc_start: 0.8874 (tppt) cc_final: 0.8463 (tppt) REVERT: A 384 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 394 PHE cc_start: 0.8600 (t80) cc_final: 0.7801 (t80) REVERT: A 422 VAL cc_start: 0.8640 (t) cc_final: 0.8270 (m) REVERT: A 426 ILE cc_start: 0.8966 (mt) cc_final: 0.8482 (tt) REVERT: A 432 MET cc_start: 0.8002 (tpt) cc_final: 0.7546 (tpt) REVERT: A 435 ILE cc_start: 0.9129 (mt) cc_final: 0.8857 (tp) REVERT: A 459 LYS cc_start: 0.9039 (tppp) cc_final: 0.8579 (tppt) REVERT: A 464 GLN cc_start: 0.8501 (tt0) cc_final: 0.7803 (tp40) REVERT: A 470 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7567 (tpp80) REVERT: A 488 MET cc_start: 0.8127 (tpp) cc_final: 0.7826 (tpp) REVERT: A 496 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 530 TYR cc_start: 0.8415 (m-10) cc_final: 0.8035 (m-10) REVERT: A 543 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 556 TYR cc_start: 0.8805 (p90) cc_final: 0.8542 (p90) REVERT: A 563 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8658 (tppp) REVERT: A 578 TYR cc_start: 0.7566 (t80) cc_final: 0.6888 (t80) REVERT: A 579 ASN cc_start: 0.8253 (p0) cc_final: 0.7691 (p0) REVERT: A 580 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8436 (mmtm) REVERT: A 583 LYS cc_start: 0.8934 (pptt) cc_final: 0.8573 (ptpt) REVERT: A 677 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7633 (ttm-80) REVERT: A 678 MET cc_start: 0.7391 (tmm) cc_final: 0.7140 (tmm) REVERT: A 681 LYS cc_start: 0.9101 (tptt) cc_final: 0.8575 (mmmm) REVERT: A 682 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 685 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8172 (mtm180) REVERT: A 687 ASP cc_start: 0.8465 (t0) cc_final: 0.8136 (t0) REVERT: A 694 LEU cc_start: 0.8775 (mm) cc_final: 0.8397 (mt) REVERT: A 698 ASP cc_start: 0.7718 (t0) cc_final: 0.7465 (t0) REVERT: A 701 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 704 GLU cc_start: 0.8082 (tt0) cc_final: 0.7725 (tt0) REVERT: A 714 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7630 (mtt90) REVERT: A 732 GLN cc_start: 0.8535 (tt0) cc_final: 0.7668 (tm-30) REVERT: B 29 GLU cc_start: 0.8675 (tp30) cc_final: 0.8363 (tp30) REVERT: B 36 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7791 (mmt-90) REVERT: B 39 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7123 (mtp85) REVERT: B 46 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7130 (tm) REVERT: B 66 LYS cc_start: 0.8948 (tppt) cc_final: 0.8565 (tppt) REVERT: B 68 LEU cc_start: 0.8930 (tp) cc_final: 0.8644 (tp) REVERT: B 73 ASP cc_start: 0.7929 (t0) cc_final: 0.7400 (t0) REVERT: B 105 TYR cc_start: 0.8734 (m-80) cc_final: 0.8239 (m-80) REVERT: B 134 ARG cc_start: 0.7660 (ptp-110) cc_final: 0.7333 (ptp-170) REVERT: B 193 THR cc_start: 0.8743 (m) cc_final: 0.8352 (p) REVERT: B 203 PHE cc_start: 0.8303 (m-80) cc_final: 0.7764 (m-80) REVERT: B 211 ILE cc_start: 0.8586 (tt) cc_final: 0.8041 (pt) REVERT: B 240 LEU cc_start: 0.9241 (mt) cc_final: 0.8767 (tt) REVERT: B 262 GLN cc_start: 0.8423 (tp40) cc_final: 0.8121 (tp-100) REVERT: B 264 ILE cc_start: 0.8910 (mm) cc_final: 0.8638 (mm) REVERT: B 273 ILE cc_start: 0.8741 (mt) cc_final: 0.8482 (pt) REVERT: B 282 CYS cc_start: 0.8765 (t) cc_final: 0.8252 (t) REVERT: B 283 MET cc_start: 0.7964 (tpp) cc_final: 0.7522 (tpp) REVERT: B 286 LYS cc_start: 0.8962 (tppt) cc_final: 0.8578 (ptmm) REVERT: B 287 GLU cc_start: 0.8458 (tp30) cc_final: 0.7632 (tp30) REVERT: B 292 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7006 (t80) REVERT: B 355 SER cc_start: 0.8867 (m) cc_final: 0.8599 (p) REVERT: B 361 TYR cc_start: 0.8765 (t80) cc_final: 0.8499 (t80) REVERT: B 369 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8383 (mtmt) REVERT: B 371 TYR cc_start: 0.7373 (m-80) cc_final: 0.6948 (m-80) REVERT: B 383 GLN cc_start: 0.8251 (tp40) cc_final: 0.7906 (tp40) REVERT: B 384 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 413 GLN cc_start: 0.7974 (pt0) cc_final: 0.7546 (tm-30) REVERT: B 421 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7933 (mm110) REVERT: B 422 VAL cc_start: 0.8553 (t) cc_final: 0.8305 (m) REVERT: B 426 ILE cc_start: 0.8912 (mt) cc_final: 0.8538 (tp) REVERT: B 432 MET cc_start: 0.8103 (tpt) cc_final: 0.7555 (tpt) REVERT: B 435 ILE cc_start: 0.9143 (mt) cc_final: 0.8898 (tp) REVERT: B 447 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8436 (mtpp) REVERT: B 464 GLN cc_start: 0.8746 (tt0) cc_final: 0.7734 (tp-100) REVERT: B 470 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7430 (tpp80) REVERT: B 473 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8546 (mppt) REVERT: B 475 ASN cc_start: 0.7138 (t0) cc_final: 0.6809 (t0) REVERT: B 486 CYS cc_start: 0.8904 (t) cc_final: 0.8662 (t) REVERT: B 495 ASP cc_start: 0.8349 (p0) cc_final: 0.8096 (p0) REVERT: B 496 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8496 (mm) REVERT: B 499 LEU cc_start: 0.8923 (tp) cc_final: 0.8615 (tp) REVERT: B 503 LEU cc_start: 0.9056 (mt) cc_final: 0.8796 (mp) REVERT: B 507 LEU cc_start: 0.8643 (tp) cc_final: 0.8401 (tt) REVERT: B 512 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8245 (mtm180) REVERT: B 537 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8329 (mmtt) REVERT: B 546 LYS cc_start: 0.7974 (tppt) cc_final: 0.7692 (tppt) REVERT: B 556 TYR cc_start: 0.8748 (p90) cc_final: 0.8529 (p90) REVERT: B 576 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: B 580 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8349 (mmtm) REVERT: B 677 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7636 (ttm-80) REVERT: B 681 LYS cc_start: 0.8826 (tptt) cc_final: 0.8237 (tppp) REVERT: B 682 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 691 TYR cc_start: 0.7864 (m-10) cc_final: 0.7566 (m-10) REVERT: B 698 ASP cc_start: 0.8030 (t0) cc_final: 0.7512 (t70) REVERT: B 701 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 714 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7607 (mtt90) REVERT: B 724 ASP cc_start: 0.8174 (t0) cc_final: 0.7485 (t70) REVERT: B 728 HIS cc_start: 0.8822 (t-170) cc_final: 0.8431 (t-170) REVERT: B 732 GLN cc_start: 0.8463 (tt0) cc_final: 0.7700 (tm-30) outliers start: 60 outliers final: 46 residues processed: 377 average time/residue: 0.1090 time to fit residues: 55.5762 Evaluate side-chains 407 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 355 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094498 restraints weight = 23165.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097828 restraints weight = 11832.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100035 restraints weight = 7216.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101564 restraints weight = 4981.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102527 restraints weight = 3784.031| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10400 Z= 0.156 Angle : 0.747 18.232 14136 Z= 0.380 Chirality : 0.044 0.177 1718 Planarity : 0.004 0.040 1758 Dihedral : 5.072 50.939 1428 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.37 % Allowed : 21.48 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1322 helix: 1.00 (0.18), residues: 828 sheet: -1.22 (0.92), residues: 36 loop : -1.95 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 685 TYR 0.049 0.002 TYR A 361 PHE 0.040 0.002 PHE A 385 TRP 0.010 0.001 TRP B 83 HIS 0.013 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00351 (10400) covalent geometry : angle 0.74662 (14136) hydrogen bonds : bond 0.04139 ( 575) hydrogen bonds : angle 3.96603 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9152 (mp) cc_final: 0.8735 (pp) REVERT: A 83 TRP cc_start: 0.6563 (m-10) cc_final: 0.6353 (m-10) REVERT: A 96 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 97 VAL cc_start: 0.9083 (t) cc_final: 0.8750 (p) REVERT: A 121 PHE cc_start: 0.8366 (t80) cc_final: 0.8010 (t80) REVERT: A 145 SER cc_start: 0.8667 (m) cc_final: 0.8225 (p) REVERT: A 160 HIS cc_start: 0.7034 (t-90) cc_final: 0.6717 (t-90) REVERT: A 161 PHE cc_start: 0.7651 (m-80) cc_final: 0.7074 (m-80) REVERT: A 235 GLN cc_start: 0.8064 (mm110) cc_final: 0.7831 (mm-40) REVERT: A 238 ILE cc_start: 0.8768 (mt) cc_final: 0.8500 (mt) REVERT: A 245 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7893 (mmtm) REVERT: A 283 MET cc_start: 0.7995 (tpp) cc_final: 0.7034 (mpp) REVERT: A 286 LYS cc_start: 0.9064 (pttp) cc_final: 0.8685 (pttp) REVERT: A 293 LYS cc_start: 0.8865 (tppt) cc_final: 0.8473 (tppt) REVERT: A 304 VAL cc_start: 0.8681 (t) cc_final: 0.8401 (p) REVERT: A 361 TYR cc_start: 0.8522 (t80) cc_final: 0.7443 (t80) REVERT: A 384 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 385 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: A 394 PHE cc_start: 0.8627 (t80) cc_final: 0.8165 (t80) REVERT: A 422 VAL cc_start: 0.8610 (t) cc_final: 0.8253 (m) REVERT: A 426 ILE cc_start: 0.8948 (mt) cc_final: 0.8497 (tt) REVERT: A 432 MET cc_start: 0.8006 (tpt) cc_final: 0.7473 (tpt) REVERT: A 435 ILE cc_start: 0.9126 (mt) cc_final: 0.8845 (tp) REVERT: A 464 GLN cc_start: 0.8439 (tt0) cc_final: 0.7835 (tp40) REVERT: A 470 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7548 (tpp80) REVERT: A 473 LYS cc_start: 0.8900 (mptt) cc_final: 0.8598 (mppt) REVERT: A 488 MET cc_start: 0.8074 (tpp) cc_final: 0.7823 (tpp) REVERT: A 496 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8590 (tp) REVERT: A 514 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 543 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 556 TYR cc_start: 0.8803 (p90) cc_final: 0.8554 (p90) REVERT: A 563 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8664 (tppp) REVERT: A 578 TYR cc_start: 0.7541 (t80) cc_final: 0.6889 (t80) REVERT: A 579 ASN cc_start: 0.8232 (p0) cc_final: 0.7691 (p0) REVERT: A 580 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8442 (mmtm) REVERT: A 583 LYS cc_start: 0.8933 (pptt) cc_final: 0.8527 (ptpt) REVERT: A 677 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7634 (ttm-80) REVERT: A 678 MET cc_start: 0.7387 (tmm) cc_final: 0.7153 (tmm) REVERT: A 681 LYS cc_start: 0.9095 (tptt) cc_final: 0.8578 (mmmm) REVERT: A 682 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 685 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8156 (mtm180) REVERT: A 687 ASP cc_start: 0.8465 (t0) cc_final: 0.8131 (t0) REVERT: A 694 LEU cc_start: 0.8757 (mm) cc_final: 0.8371 (mt) REVERT: A 698 ASP cc_start: 0.7792 (t0) cc_final: 0.7480 (t0) REVERT: A 701 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 704 GLU cc_start: 0.8065 (tt0) cc_final: 0.7704 (tt0) REVERT: A 714 ARG cc_start: 0.7896 (ptp90) cc_final: 0.7610 (mtt90) REVERT: A 732 GLN cc_start: 0.8522 (tt0) cc_final: 0.7662 (tm-30) REVERT: B 29 GLU cc_start: 0.8683 (tp30) cc_final: 0.8374 (tp30) REVERT: B 36 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7782 (mmt-90) REVERT: B 39 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7252 (ttm110) REVERT: B 46 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7134 (tm) REVERT: B 66 LYS cc_start: 0.8931 (tppt) cc_final: 0.8510 (tppt) REVERT: B 68 LEU cc_start: 0.8937 (tp) cc_final: 0.8649 (tp) REVERT: B 73 ASP cc_start: 0.7925 (t0) cc_final: 0.7481 (t0) REVERT: B 105 TYR cc_start: 0.8710 (m-80) cc_final: 0.8196 (m-80) REVERT: B 134 ARG cc_start: 0.7768 (ptp-110) cc_final: 0.7328 (ptp-170) REVERT: B 193 THR cc_start: 0.8649 (m) cc_final: 0.8248 (p) REVERT: B 203 PHE cc_start: 0.8287 (m-80) cc_final: 0.7757 (m-80) REVERT: B 211 ILE cc_start: 0.8583 (tt) cc_final: 0.8071 (pt) REVERT: B 213 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7549 (mtm-85) REVERT: B 240 LEU cc_start: 0.9230 (mt) cc_final: 0.8753 (tt) REVERT: B 262 GLN cc_start: 0.8416 (tp40) cc_final: 0.8097 (tp-100) REVERT: B 264 ILE cc_start: 0.8908 (mm) cc_final: 0.8653 (mm) REVERT: B 266 ASP cc_start: 0.7874 (m-30) cc_final: 0.7281 (p0) REVERT: B 273 ILE cc_start: 0.8766 (mt) cc_final: 0.8501 (pt) REVERT: B 282 CYS cc_start: 0.8776 (t) cc_final: 0.8469 (t) REVERT: B 287 GLU cc_start: 0.8434 (tp30) cc_final: 0.7557 (tp30) REVERT: B 292 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 355 SER cc_start: 0.8857 (m) cc_final: 0.8585 (p) REVERT: B 361 TYR cc_start: 0.8748 (t80) cc_final: 0.8475 (t80) REVERT: B 369 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8381 (mtmt) REVERT: B 371 TYR cc_start: 0.7342 (m-80) cc_final: 0.6957 (m-80) REVERT: B 383 GLN cc_start: 0.8240 (tp40) cc_final: 0.7909 (tp40) REVERT: B 384 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 413 GLN cc_start: 0.7974 (pt0) cc_final: 0.7533 (tm-30) REVERT: B 421 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7899 (mm110) REVERT: B 422 VAL cc_start: 0.8542 (t) cc_final: 0.8291 (m) REVERT: B 426 ILE cc_start: 0.8912 (mt) cc_final: 0.8537 (tp) REVERT: B 432 MET cc_start: 0.8090 (tpt) cc_final: 0.7535 (tpt) REVERT: B 435 ILE cc_start: 0.9142 (mt) cc_final: 0.8892 (tp) REVERT: B 447 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8410 (mtpp) REVERT: B 464 GLN cc_start: 0.8727 (tt0) cc_final: 0.8014 (tp-100) REVERT: B 470 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7364 (tpp80) REVERT: B 473 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8544 (mppt) REVERT: B 475 ASN cc_start: 0.7157 (t0) cc_final: 0.5596 (t0) REVERT: B 478 ASP cc_start: 0.7973 (m-30) cc_final: 0.7279 (m-30) REVERT: B 486 CYS cc_start: 0.8884 (t) cc_final: 0.8643 (t) REVERT: B 496 LEU cc_start: 0.8858 (mm) cc_final: 0.8622 (mm) REVERT: B 499 LEU cc_start: 0.8915 (tp) cc_final: 0.8612 (tp) REVERT: B 503 LEU cc_start: 0.9051 (mt) cc_final: 0.8804 (mp) REVERT: B 507 LEU cc_start: 0.8631 (tp) cc_final: 0.8391 (tt) REVERT: B 512 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8202 (mtm180) REVERT: B 528 ASP cc_start: 0.8224 (p0) cc_final: 0.7707 (p0) REVERT: B 556 TYR cc_start: 0.8727 (p90) cc_final: 0.8441 (p90) REVERT: B 565 CYS cc_start: 0.7740 (p) cc_final: 0.7528 (p) REVERT: B 576 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: B 580 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8353 (mmtm) REVERT: B 669 ASP cc_start: 0.7165 (t0) cc_final: 0.6836 (t0) REVERT: B 677 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7625 (ttm-80) REVERT: B 681 LYS cc_start: 0.8810 (tptt) cc_final: 0.8438 (ttmm) REVERT: B 682 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8375 (tm-30) REVERT: B 691 TYR cc_start: 0.7842 (m-10) cc_final: 0.7546 (m-10) REVERT: B 698 ASP cc_start: 0.7955 (t0) cc_final: 0.7514 (t0) REVERT: B 701 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 714 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7601 (mtt90) REVERT: B 724 ASP cc_start: 0.8144 (t0) cc_final: 0.7507 (t70) REVERT: B 728 HIS cc_start: 0.8793 (t-170) cc_final: 0.8420 (t-170) REVERT: B 732 GLN cc_start: 0.8438 (tt0) cc_final: 0.7714 (tm-30) outliers start: 49 outliers final: 39 residues processed: 385 average time/residue: 0.1093 time to fit residues: 56.9376 Evaluate side-chains 396 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 351 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092827 restraints weight = 23415.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096111 restraints weight = 11947.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098195 restraints weight = 7271.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099708 restraints weight = 5086.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.100786 restraints weight = 3874.773| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 10400 Z= 0.208 Angle : 0.788 18.986 14136 Z= 0.401 Chirality : 0.046 0.174 1718 Planarity : 0.004 0.044 1758 Dihedral : 5.087 52.057 1426 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.81 % Allowed : 22.01 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1322 helix: 0.92 (0.18), residues: 846 sheet: -1.88 (0.76), residues: 48 loop : -1.94 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.042 0.002 TYR A 361 PHE 0.035 0.002 PHE A 385 TRP 0.025 0.002 TRP B 83 HIS 0.016 0.002 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00447 (10400) covalent geometry : angle 0.78824 (14136) hydrogen bonds : bond 0.04323 ( 575) hydrogen bonds : angle 4.03631 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.58 seconds wall clock time: 33 minutes 51.81 seconds (2031.81 seconds total)