Starting phenix.real_space_refine on Mon Jun 9 03:27:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_32576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_32576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_32576.map" model { file = "/net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_32576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl7_32576/06_2025/7wl7_32576.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.24, per 1000 atoms: 0.61 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.75 Time building geometry restraints manager: 2.96 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: 0.05 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.130 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP A 83 HIS 0.001 0.000 HIS A 723 PHE 0.008 0.001 PHE B 555 TYR 0.007 0.001 TYR B 127 ARG 0.001 0.000 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.22873 ( 575) hydrogen bonds : angle 6.63054 ( 1683) covalent geometry : bond 0.00176 (10400) covalent geometry : angle 0.49539 (14136) *********************** 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 : 1.205 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: 0.7845 (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: 0.7692 (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: 0.7874 (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: 0.8117 (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: 0.8195 (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: 0.7733 (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: 0.7098 (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: 0.8696 (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: 0.7142 (p0) REVERT: B 271 ASP cc_start: 0.7617 (m-30) cc_final: 0.7370 (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: 0.8452 (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: 0.7563 (pp) REVERT: B 537 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8169 (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: 0.7686 (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: 0.2819 time to fit residues: 153.8177 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 : 1.193 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 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 = 0.3745 r_free = 0.3745 target = 0.114489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096960 restraints weight = 23160.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100239 restraints weight = 11852.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102463 restraints weight = 7305.111| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10400 Z= 0.170 Angle : 0.671 11.430 14136 Z= 0.347 Chirality : 0.043 0.167 1718 Planarity : 0.005 0.036 1758 Dihedral : 6.274 83.141 1445 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.63 % Allowed : 12.03 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.22), residues: 1322 helix: -0.14 (0.17), residues: 834 sheet: -3.02 (0.67), residues: 48 loop : -2.65 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.010 0.002 HIS B 728 PHE 0.023 0.002 PHE B 385 TYR 0.020 0.002 TYR A 377 ARG 0.006 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 575) hydrogen bonds : angle 4.15522 ( 1683) covalent geometry : bond 0.00348 (10400) covalent geometry : angle 0.67150 (14136) *********************** 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 414 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 362 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7077 (ttm110) REVERT: A 46 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7114 (tm) REVERT: A 66 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8234 (mmmm) REVERT: A 83 TRP cc_start: 0.6556 (m-10) cc_final: 0.6334 (m-10) REVERT: A 121 PHE cc_start: 0.8394 (t80) cc_final: 0.8088 (t80) REVERT: A 122 PHE cc_start: 0.8298 (m-80) cc_final: 0.7802 (m-10) REVERT: A 145 SER cc_start: 0.8636 (m) cc_final: 0.8182 (p) REVERT: A 160 HIS cc_start: 0.7131 (t-90) cc_final: 0.6582 (t-90) REVERT: A 161 PHE cc_start: 0.7611 (m-80) cc_final: 0.6602 (m-80) REVERT: A 182 ASP cc_start: 0.8352 (m-30) cc_final: 0.7975 (m-30) REVERT: A 213 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7534 (ptp-170) REVERT: A 229 PHE cc_start: 0.8571 (t80) cc_final: 0.8350 (t80) REVERT: A 235 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (mm-40) REVERT: A 238 ILE cc_start: 0.8641 (mt) cc_final: 0.8334 (tp) REVERT: A 242 VAL cc_start: 0.9058 (m) cc_final: 0.8776 (p) REVERT: A 259 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8144 (pp20) REVERT: A 292 PHE cc_start: 0.7531 (t80) cc_final: 0.7258 (t80) REVERT: A 293 LYS cc_start: 0.8846 (tppt) cc_final: 0.8603 (tppt) REVERT: A 361 TYR cc_start: 0.8729 (t80) cc_final: 0.8498 (t80) REVERT: A 384 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 394 PHE cc_start: 0.8456 (t80) cc_final: 0.6929 (t80) REVERT: A 398 PHE cc_start: 0.6732 (m-80) cc_final: 0.5970 (m-80) REVERT: A 422 VAL cc_start: 0.8599 (t) cc_final: 0.8243 (m) REVERT: A 432 MET cc_start: 0.8094 (tpt) cc_final: 0.7652 (tpt) REVERT: A 435 ILE cc_start: 0.9125 (mt) cc_final: 0.8796 (tp) REVERT: A 459 LYS cc_start: 0.8955 (tppp) cc_final: 0.8555 (tppt) REVERT: A 470 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7418 (tpp80) REVERT: A 496 LEU cc_start: 0.8899 (mm) cc_final: 0.8623 (mm) REVERT: A 529 ILE cc_start: 0.8137 (tp) cc_final: 0.7822 (pt) REVERT: A 537 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8134 (mtpp) REVERT: A 556 TYR cc_start: 0.8700 (p90) cc_final: 0.8445 (p90) REVERT: A 576 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7473 (mtm-85) REVERT: A 578 TYR cc_start: 0.7531 (t80) cc_final: 0.7025 (t80) REVERT: A 580 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8640 (mmtm) REVERT: A 582 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 677 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7670 (ttm-80) REVERT: A 678 MET cc_start: 0.7157 (tmm) cc_final: 0.5659 (tmm) REVERT: A 681 LYS cc_start: 0.9036 (tptt) cc_final: 0.8483 (mmmm) REVERT: A 685 ARG cc_start: 0.8637 (mtm180) cc_final: 0.8251 (mtm180) REVERT: A 687 ASP cc_start: 0.8483 (t0) cc_final: 0.8029 (t0) REVERT: A 698 ASP cc_start: 0.7641 (t0) cc_final: 0.7394 (t0) REVERT: A 701 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 704 GLU cc_start: 0.8124 (tt0) cc_final: 0.7723 (tt0) REVERT: A 714 ARG cc_start: 0.7928 (ptp90) cc_final: 0.7638 (mtt90) REVERT: A 732 GLN cc_start: 0.8536 (tt0) cc_final: 0.7581 (tm-30) REVERT: B 36 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7818 (mmt-90) REVERT: B 37 GLU cc_start: 0.7931 (pm20) cc_final: 0.7724 (pm20) REVERT: B 46 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7104 (tm) REVERT: B 68 LEU cc_start: 0.8909 (tp) cc_final: 0.8611 (tp) REVERT: B 73 ASP cc_start: 0.7915 (t0) cc_final: 0.7629 (t0) REVERT: B 96 LEU cc_start: 0.9090 (mt) cc_final: 0.8795 (mm) REVERT: B 121 PHE cc_start: 0.7755 (t80) cc_final: 0.7476 (t80) REVERT: B 161 PHE cc_start: 0.7827 (m-80) cc_final: 0.6983 (m-80) REVERT: B 199 ILE cc_start: 0.9189 (mt) cc_final: 0.8970 (mt) REVERT: B 203 PHE cc_start: 0.8447 (m-80) cc_final: 0.7668 (m-80) REVERT: B 211 ILE cc_start: 0.8634 (tt) cc_final: 0.7952 (pt) REVERT: B 235 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7959 (mm-40) REVERT: B 264 ILE cc_start: 0.8631 (mm) cc_final: 0.8378 (mm) REVERT: B 271 ASP cc_start: 0.8179 (m-30) cc_final: 0.7958 (m-30) REVERT: B 273 ILE cc_start: 0.8725 (mt) cc_final: 0.8489 (pt) REVERT: B 276 LEU cc_start: 0.8713 (tp) cc_final: 0.8432 (tt) REVERT: B 282 CYS cc_start: 0.8668 (t) cc_final: 0.8451 (t) REVERT: B 287 GLU cc_start: 0.8603 (tp30) cc_final: 0.7691 (tp30) REVERT: B 288 LEU cc_start: 0.8955 (tp) cc_final: 0.8740 (tp) REVERT: B 292 PHE cc_start: 0.7559 (t80) cc_final: 0.7283 (t80) REVERT: B 293 LYS cc_start: 0.8081 (tppt) cc_final: 0.7627 (tppt) REVERT: B 355 SER cc_start: 0.9062 (m) cc_final: 0.8742 (p) REVERT: B 369 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8451 (mtmt) REVERT: B 383 GLN cc_start: 0.8424 (tp40) cc_final: 0.7905 (tp40) REVERT: B 384 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7405 (mm-30) REVERT: B 421 GLN cc_start: 0.8244 (mm110) cc_final: 0.7950 (mm110) REVERT: B 426 ILE cc_start: 0.8800 (mt) cc_final: 0.8447 (tp) REVERT: B 432 MET cc_start: 0.8122 (tpt) cc_final: 0.7605 (tpt) REVERT: B 435 ILE cc_start: 0.8958 (mt) cc_final: 0.8636 (tp) REVERT: B 447 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8485 (mtpp) REVERT: B 470 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7370 (tpp80) REVERT: B 473 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8564 (mppt) REVERT: B 475 ASN cc_start: 0.7212 (t0) cc_final: 0.6832 (t0) REVERT: B 484 PHE cc_start: 0.8610 (t80) cc_final: 0.8142 (t80) REVERT: B 486 CYS cc_start: 0.9033 (t) cc_final: 0.8788 (t) REVERT: B 503 LEU cc_start: 0.9002 (mt) cc_final: 0.8798 (mm) REVERT: B 546 LYS cc_start: 0.8035 (tppt) cc_final: 0.7804 (tppt) REVERT: B 580 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8442 (mmtm) REVERT: B 677 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7683 (ttm-80) REVERT: B 678 MET cc_start: 0.7464 (tpp) cc_final: 0.6866 (tpp) REVERT: B 681 LYS cc_start: 0.9078 (tptt) cc_final: 0.8538 (mmmm) REVERT: B 697 ASP cc_start: 0.7917 (m-30) cc_final: 0.7651 (m-30) REVERT: B 698 ASP cc_start: 0.8007 (t0) cc_final: 0.7563 (t0) REVERT: B 701 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 714 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7524 (mtt90) REVERT: B 727 LEU cc_start: 0.8754 (mt) cc_final: 0.8221 (mt) REVERT: B 732 GLN cc_start: 0.8218 (tt0) cc_final: 0.7333 (tm-30) outliers start: 52 outliers final: 27 residues processed: 387 average time/residue: 0.2380 time to fit residues: 124.2443 Evaluate side-chains 379 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 347 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 235 GLN 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 433 VAL 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 51 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096211 restraints weight = 23508.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099551 restraints weight = 12062.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101749 restraints weight = 7386.758| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10400 Z= 0.147 Angle : 0.630 10.992 14136 Z= 0.322 Chirality : 0.042 0.161 1718 Planarity : 0.004 0.037 1758 Dihedral : 5.309 58.114 1434 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.19 % Allowed : 14.53 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1322 helix: 0.48 (0.18), residues: 848 sheet: -2.26 (0.87), residues: 36 loop : -2.50 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.010 0.002 HIS B 728 PHE 0.021 0.001 PHE A 354 TYR 0.015 0.001 TYR A 377 ARG 0.007 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 575) hydrogen bonds : angle 3.97809 ( 1683) covalent geometry : bond 0.00311 (10400) covalent geometry : angle 0.63022 (14136) *********************** 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 385 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 1.058 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: A 27 TYR cc_start: 0.8224 (m-10) cc_final: 0.7988 (m-10) REVERT: A 29 GLU cc_start: 0.8450 (tp30) cc_final: 0.8236 (tp30) REVERT: A 37 GLU cc_start: 0.8079 (pm20) cc_final: 0.7632 (pm20) REVERT: A 46 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7135 (tm) REVERT: A 83 TRP cc_start: 0.6553 (m-10) cc_final: 0.6281 (m-10) REVERT: A 96 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8878 (mm) REVERT: A 97 VAL cc_start: 0.9050 (t) cc_final: 0.8786 (p) REVERT: A 121 PHE cc_start: 0.8356 (t80) cc_final: 0.7969 (t80) REVERT: A 122 PHE cc_start: 0.8235 (m-80) cc_final: 0.7779 (m-10) REVERT: A 145 SER cc_start: 0.8702 (m) cc_final: 0.8230 (p) REVERT: A 160 HIS cc_start: 0.6993 (t-90) cc_final: 0.6445 (t-90) REVERT: A 161 PHE cc_start: 0.7623 (m-80) cc_final: 0.6728 (m-80) REVERT: A 182 ASP cc_start: 0.8325 (m-30) cc_final: 0.7992 (m-30) REVERT: A 229 PHE cc_start: 0.8594 (t80) cc_final: 0.8353 (t80) REVERT: A 235 GLN cc_start: 0.8164 (mm110) cc_final: 0.7895 (mm-40) REVERT: A 238 ILE cc_start: 0.8718 (mt) cc_final: 0.8361 (tp) REVERT: A 242 VAL cc_start: 0.9030 (m) cc_final: 0.8725 (p) REVERT: A 258 ILE cc_start: 0.8819 (mm) cc_final: 0.8508 (tp) REVERT: A 292 PHE cc_start: 0.7585 (t80) cc_final: 0.7276 (t80) REVERT: A 293 LYS cc_start: 0.8903 (tppt) cc_final: 0.8524 (tppt) REVERT: A 320 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7735 (pp20) REVERT: A 384 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 394 PHE cc_start: 0.8481 (t80) cc_final: 0.7696 (t80) REVERT: A 432 MET cc_start: 0.8002 (tpt) cc_final: 0.7560 (tpt) REVERT: A 435 ILE cc_start: 0.9097 (mt) cc_final: 0.8804 (tp) REVERT: A 470 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7482 (tpp80) REVERT: A 496 LEU cc_start: 0.8944 (mm) cc_final: 0.8587 (mm) REVERT: A 529 ILE cc_start: 0.8172 (tp) cc_final: 0.7919 (pt) REVERT: A 537 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8079 (mtpp) REVERT: A 556 TYR cc_start: 0.8710 (p90) cc_final: 0.8444 (p90) REVERT: A 578 TYR cc_start: 0.7495 (t80) cc_final: 0.6875 (t80) REVERT: A 580 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8630 (mmtm) REVERT: A 582 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8800 (mm) REVERT: A 677 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7659 (ttm-80) REVERT: A 678 MET cc_start: 0.7283 (tmm) cc_final: 0.6568 (tmm) REVERT: A 681 LYS cc_start: 0.9035 (tptt) cc_final: 0.8501 (mmmm) REVERT: A 682 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 685 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8185 (mtm110) REVERT: A 687 ASP cc_start: 0.8451 (t0) cc_final: 0.7992 (t0) REVERT: A 694 LEU cc_start: 0.8759 (mm) cc_final: 0.8418 (mt) REVERT: A 701 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 704 GLU cc_start: 0.8136 (tt0) cc_final: 0.7701 (tt0) REVERT: A 714 ARG cc_start: 0.7888 (ptp90) cc_final: 0.7558 (mtt90) REVERT: A 732 GLN cc_start: 0.8471 (tt0) cc_final: 0.7515 (tm-30) REVERT: B 36 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7774 (mpt180) REVERT: B 37 GLU cc_start: 0.7953 (pm20) cc_final: 0.7709 (pm20) REVERT: B 46 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7163 (tm) REVERT: B 68 LEU cc_start: 0.8918 (tp) cc_final: 0.8664 (tp) REVERT: B 73 ASP cc_start: 0.7971 (t0) cc_final: 0.7685 (t0) REVERT: B 130 PHE cc_start: 0.8182 (m-80) cc_final: 0.7803 (m-10) REVERT: B 161 PHE cc_start: 0.7783 (m-80) cc_final: 0.7183 (m-80) REVERT: B 203 PHE cc_start: 0.8460 (m-80) cc_final: 0.7706 (m-80) REVERT: B 211 ILE cc_start: 0.8644 (tt) cc_final: 0.7950 (pt) REVERT: B 264 ILE cc_start: 0.8801 (mm) cc_final: 0.8511 (mm) REVERT: B 273 ILE cc_start: 0.8725 (mt) cc_final: 0.8495 (pt) REVERT: B 276 LEU cc_start: 0.8687 (tp) cc_final: 0.8411 (tt) REVERT: B 282 CYS cc_start: 0.8715 (t) cc_final: 0.8216 (t) REVERT: B 283 MET cc_start: 0.7961 (tpp) cc_final: 0.7228 (tpp) REVERT: B 286 LYS cc_start: 0.8957 (tppt) cc_final: 0.8521 (ptmm) REVERT: B 291 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7535 (ttp-110) REVERT: B 292 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 293 LYS cc_start: 0.8071 (tppt) cc_final: 0.7564 (tppt) REVERT: B 355 SER cc_start: 0.9010 (m) cc_final: 0.8743 (p) REVERT: B 383 GLN cc_start: 0.8361 (tp40) cc_final: 0.7868 (tp40) REVERT: B 384 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 413 GLN cc_start: 0.8067 (pt0) cc_final: 0.7439 (pp30) REVERT: B 421 GLN cc_start: 0.8173 (mm110) cc_final: 0.7973 (mm110) REVERT: B 426 ILE cc_start: 0.8830 (mt) cc_final: 0.8487 (tp) REVERT: B 432 MET cc_start: 0.8152 (tpt) cc_final: 0.7751 (tpt) REVERT: B 435 ILE cc_start: 0.9020 (mt) cc_final: 0.8752 (tp) REVERT: B 447 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8453 (mtpp) REVERT: B 470 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7406 (tpp80) REVERT: B 473 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8541 (mppt) REVERT: B 475 ASN cc_start: 0.7167 (t0) cc_final: 0.6726 (t0) REVERT: B 486 CYS cc_start: 0.9024 (t) cc_final: 0.8764 (t) REVERT: B 495 ASP cc_start: 0.8357 (p0) cc_final: 0.8064 (p0) REVERT: B 496 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8477 (mm) REVERT: B 499 LEU cc_start: 0.8841 (tp) cc_final: 0.8609 (tp) REVERT: B 503 LEU cc_start: 0.9008 (mt) cc_final: 0.8725 (mp) REVERT: B 507 LEU cc_start: 0.8629 (tp) cc_final: 0.8372 (tt) REVERT: B 537 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8377 (ttmm) REVERT: B 546 LYS cc_start: 0.8079 (tppt) cc_final: 0.7731 (tppt) REVERT: B 578 TYR cc_start: 0.7686 (t80) cc_final: 0.7463 (t80) REVERT: B 580 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8373 (mmtm) REVERT: B 668 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.6359 (tp) REVERT: B 677 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7684 (ttm-80) REVERT: B 678 MET cc_start: 0.7497 (tpp) cc_final: 0.6902 (tpp) REVERT: B 681 LYS cc_start: 0.9057 (tptt) cc_final: 0.8513 (mmmm) REVERT: B 698 ASP cc_start: 0.7988 (t0) cc_final: 0.7540 (t0) REVERT: B 701 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 705 GLN cc_start: 0.8535 (mt0) cc_final: 0.8318 (pp30) REVERT: B 714 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7495 (mtt90) REVERT: B 727 LEU cc_start: 0.8731 (mt) cc_final: 0.8407 (mt) REVERT: B 732 GLN cc_start: 0.8141 (tt0) cc_final: 0.7281 (tm-30) outliers start: 47 outliers final: 31 residues processed: 362 average time/residue: 0.2509 time to fit residues: 121.6687 Evaluate side-chains 364 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 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 262 GLN 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 405 THR Chi-restraints excluded: chain B residue 433 VAL 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 85 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 262 GLN ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096066 restraints weight = 23049.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099284 restraints weight = 11777.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101427 restraints weight = 7211.064| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10400 Z= 0.158 Angle : 0.641 10.467 14136 Z= 0.327 Chirality : 0.042 0.198 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.295 58.932 1434 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.55 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1322 helix: 0.70 (0.18), residues: 848 sheet: -2.12 (0.88), residues: 36 loop : -2.33 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 83 HIS 0.011 0.002 HIS B 728 PHE 0.024 0.001 PHE A 484 TYR 0.017 0.001 TYR A 361 ARG 0.009 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 575) hydrogen bonds : angle 3.88852 ( 1683) covalent geometry : bond 0.00331 (10400) covalent geometry : angle 0.64079 (14136) *********************** 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 377 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 1.062 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: A 27 TYR cc_start: 0.8298 (m-10) cc_final: 0.8062 (m-10) REVERT: A 37 GLU cc_start: 0.8105 (pm20) cc_final: 0.7612 (pm20) REVERT: A 66 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8082 (mmtt) REVERT: A 72 LEU cc_start: 0.9164 (mp) cc_final: 0.8953 (pt) REVERT: A 83 TRP cc_start: 0.6561 (m-10) cc_final: 0.6283 (m-10) REVERT: A 94 THR cc_start: 0.8597 (p) cc_final: 0.8010 (p) REVERT: A 96 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 97 VAL cc_start: 0.9098 (t) cc_final: 0.8800 (p) REVERT: A 121 PHE cc_start: 0.8355 (t80) cc_final: 0.7810 (t80) REVERT: A 122 PHE cc_start: 0.8253 (m-80) cc_final: 0.7689 (m-10) REVERT: A 134 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: A 145 SER cc_start: 0.8709 (m) cc_final: 0.8251 (p) REVERT: A 160 HIS cc_start: 0.7042 (t-90) cc_final: 0.6713 (t-90) REVERT: A 161 PHE cc_start: 0.7661 (m-80) cc_final: 0.7011 (m-80) REVERT: A 182 ASP cc_start: 0.8370 (m-30) cc_final: 0.8042 (m-30) REVERT: A 229 PHE cc_start: 0.8595 (t80) cc_final: 0.8328 (t80) REVERT: A 235 GLN cc_start: 0.8151 (mm110) cc_final: 0.7886 (mm-40) REVERT: A 238 ILE cc_start: 0.8739 (mt) cc_final: 0.8465 (mt) REVERT: A 242 VAL cc_start: 0.9029 (m) cc_final: 0.8707 (p) REVERT: A 258 ILE cc_start: 0.8822 (mm) cc_final: 0.8528 (tp) REVERT: A 292 PHE cc_start: 0.7658 (t80) cc_final: 0.7350 (t80) REVERT: A 293 LYS cc_start: 0.8911 (tppt) cc_final: 0.8507 (tppt) REVERT: A 361 TYR cc_start: 0.8714 (t80) cc_final: 0.8403 (t80) REVERT: A 384 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 385 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (t80) REVERT: A 394 PHE cc_start: 0.8531 (t80) cc_final: 0.7642 (t80) REVERT: A 426 ILE cc_start: 0.8945 (mt) cc_final: 0.8486 (tt) REVERT: A 432 MET cc_start: 0.8024 (tpt) cc_final: 0.7441 (tpt) REVERT: A 435 ILE cc_start: 0.9122 (mt) cc_final: 0.8814 (tp) REVERT: A 470 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7504 (tpp80) REVERT: A 495 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 496 LEU cc_start: 0.8961 (mm) cc_final: 0.8468 (mm) REVERT: A 526 SER cc_start: 0.8466 (t) cc_final: 0.8149 (p) REVERT: A 529 ILE cc_start: 0.8175 (tp) cc_final: 0.7858 (pt) REVERT: A 537 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8259 (ttmm) REVERT: A 543 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 556 TYR cc_start: 0.8740 (p90) cc_final: 0.8416 (p90) REVERT: A 563 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8714 (tppp) REVERT: A 578 TYR cc_start: 0.7486 (t80) cc_final: 0.6993 (t80) REVERT: A 580 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8655 (mmtm) REVERT: A 582 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 678 MET cc_start: 0.7247 (tmm) cc_final: 0.6850 (tmm) REVERT: A 681 LYS cc_start: 0.9055 (tptt) cc_final: 0.8531 (mmmm) REVERT: A 685 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8248 (mtm180) REVERT: A 687 ASP cc_start: 0.8427 (t0) cc_final: 0.8116 (t0) REVERT: A 694 LEU cc_start: 0.8760 (mm) cc_final: 0.8408 (mt) REVERT: A 701 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 704 GLU cc_start: 0.8146 (tt0) cc_final: 0.7675 (tt0) REVERT: A 714 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7615 (mtt90) REVERT: A 732 GLN cc_start: 0.8450 (tt0) cc_final: 0.7527 (tm-30) REVERT: B 36 ARG cc_start: 0.8210 (tpp-160) cc_final: 0.7784 (mpt180) REVERT: B 37 GLU cc_start: 0.7963 (pm20) cc_final: 0.7731 (pm20) REVERT: B 46 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7165 (tm) REVERT: B 68 LEU cc_start: 0.8921 (tp) cc_final: 0.8653 (tp) REVERT: B 73 ASP cc_start: 0.7963 (t0) cc_final: 0.7649 (t0) REVERT: B 96 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8814 (mm) REVERT: B 161 PHE cc_start: 0.7912 (m-80) cc_final: 0.7333 (m-10) REVERT: B 203 PHE cc_start: 0.8415 (m-80) cc_final: 0.7809 (m-80) REVERT: B 211 ILE cc_start: 0.8655 (tt) cc_final: 0.8061 (pt) REVERT: B 213 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7350 (mtm-85) REVERT: B 264 ILE cc_start: 0.8819 (mm) cc_final: 0.8545 (mm) REVERT: B 273 ILE cc_start: 0.8709 (mt) cc_final: 0.8487 (pt) REVERT: B 276 LEU cc_start: 0.8713 (tp) cc_final: 0.8431 (tt) REVERT: B 282 CYS cc_start: 0.8725 (t) cc_final: 0.8452 (t) REVERT: B 291 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7512 (ttp-110) REVERT: B 292 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 293 LYS cc_start: 0.8125 (tppt) cc_final: 0.7611 (tppt) REVERT: B 355 SER cc_start: 0.9017 (m) cc_final: 0.8740 (p) REVERT: B 369 LYS cc_start: 0.8752 (pttt) cc_final: 0.8304 (mmmt) REVERT: B 371 TYR cc_start: 0.7499 (m-80) cc_final: 0.7058 (m-80) REVERT: B 383 GLN cc_start: 0.8341 (tp40) cc_final: 0.7906 (tp40) REVERT: B 384 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 413 GLN cc_start: 0.8080 (pt0) cc_final: 0.7465 (pp30) REVERT: B 426 ILE cc_start: 0.8850 (mt) cc_final: 0.8501 (tp) REVERT: B 432 MET cc_start: 0.8232 (tpt) cc_final: 0.7613 (tpt) REVERT: B 435 ILE cc_start: 0.9090 (mt) cc_final: 0.8791 (tp) REVERT: B 447 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8536 (mtpp) REVERT: B 470 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7428 (tpp80) REVERT: B 473 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8557 (mppt) REVERT: B 475 ASN cc_start: 0.7122 (t0) cc_final: 0.6734 (t0) REVERT: B 486 CYS cc_start: 0.8985 (t) cc_final: 0.8724 (t) REVERT: B 496 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 503 LEU cc_start: 0.9012 (mt) cc_final: 0.8807 (mm) REVERT: B 507 LEU cc_start: 0.8634 (tp) cc_final: 0.8362 (tt) REVERT: B 512 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8175 (mtm110) REVERT: B 537 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8371 (ttmm) REVERT: B 546 LYS cc_start: 0.8062 (tppt) cc_final: 0.7749 (tppt) REVERT: B 580 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8382 (mmtm) REVERT: B 587 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6816 (tpt170) REVERT: B 677 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7662 (ttm-80) REVERT: B 678 MET cc_start: 0.7532 (tpp) cc_final: 0.6883 (tpp) REVERT: B 681 LYS cc_start: 0.9070 (tptt) cc_final: 0.8309 (mmmm) REVERT: B 685 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8083 (mtm-85) REVERT: B 698 ASP cc_start: 0.7991 (t0) cc_final: 0.7679 (t70) REVERT: B 701 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 714 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7532 (mtt90) REVERT: B 727 LEU cc_start: 0.8722 (mt) cc_final: 0.8521 (mt) REVERT: B 732 GLN cc_start: 0.8146 (tt0) cc_final: 0.7278 (tm-30) outliers start: 51 outliers final: 36 residues processed: 355 average time/residue: 0.2522 time to fit residues: 119.9509 Evaluate side-chains 366 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 253 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 495 ASP 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 71 ILE Chi-restraints excluded: chain B residue 72 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 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 375 HIS Chi-restraints excluded: chain B residue 433 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 131 optimal weight: 0.1980 overall best weight: 0.1742 ------------------------------------------------------------------------------- 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** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097855 restraints weight = 23002.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101104 restraints weight = 11721.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103285 restraints weight = 7212.792| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.127 Angle : 0.635 9.980 14136 Z= 0.321 Chirality : 0.041 0.212 1718 Planarity : 0.004 0.034 1758 Dihedral : 5.168 55.599 1432 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.37 % Allowed : 17.47 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1322 helix: 0.92 (0.18), residues: 822 sheet: -1.93 (0.88), residues: 36 loop : -2.10 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 83 HIS 0.017 0.002 HIS A 375 PHE 0.035 0.001 PHE B 121 TYR 0.016 0.001 TYR B 377 ARG 0.005 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 575) hydrogen bonds : angle 3.79386 ( 1683) covalent geometry : bond 0.00277 (10400) covalent geometry : angle 0.63533 (14136) *********************** 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 383 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 1.216 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 27 TYR cc_start: 0.8239 (m-10) cc_final: 0.8022 (m-10) REVERT: A 37 GLU cc_start: 0.8069 (pm20) cc_final: 0.7584 (pm20) REVERT: A 39 ARG cc_start: 0.7403 (ttm110) cc_final: 0.6768 (mtp85) REVERT: A 66 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8072 (mmtt) REVERT: A 83 TRP cc_start: 0.6519 (m-10) cc_final: 0.6301 (m-10) REVERT: A 96 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8915 (mm) REVERT: A 97 VAL cc_start: 0.9099 (t) cc_final: 0.8784 (p) REVERT: A 121 PHE cc_start: 0.8328 (t80) cc_final: 0.7917 (t80) REVERT: A 122 PHE cc_start: 0.8241 (m-80) cc_final: 0.7744 (m-80) REVERT: A 145 SER cc_start: 0.8693 (m) cc_final: 0.8218 (p) REVERT: A 160 HIS cc_start: 0.7012 (t-90) cc_final: 0.6708 (t-90) REVERT: A 161 PHE cc_start: 0.7610 (m-80) cc_final: 0.6946 (m-80) REVERT: A 182 ASP cc_start: 0.8323 (m-30) cc_final: 0.7987 (m-30) REVERT: A 213 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.7281 (ptp-110) REVERT: A 229 PHE cc_start: 0.8592 (t80) cc_final: 0.8333 (t80) REVERT: A 235 GLN cc_start: 0.8074 (mm110) cc_final: 0.7811 (mm-40) REVERT: A 238 ILE cc_start: 0.8731 (mt) cc_final: 0.8370 (tp) REVERT: A 242 VAL cc_start: 0.9032 (m) cc_final: 0.8701 (p) REVERT: A 258 ILE cc_start: 0.8825 (mm) cc_final: 0.8525 (tp) REVERT: A 283 MET cc_start: 0.8201 (tpp) cc_final: 0.6937 (mpp) REVERT: A 292 PHE cc_start: 0.7628 (t80) cc_final: 0.7279 (t80) REVERT: A 293 LYS cc_start: 0.8890 (tppt) cc_final: 0.8496 (tppt) REVERT: A 320 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7671 (pp20) REVERT: A 361 TYR cc_start: 0.8667 (t80) cc_final: 0.8356 (t80) REVERT: A 384 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 385 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8568 (t80) REVERT: A 394 PHE cc_start: 0.8550 (t80) cc_final: 0.7564 (t80) REVERT: A 422 VAL cc_start: 0.8595 (t) cc_final: 0.8234 (m) REVERT: A 426 ILE cc_start: 0.8927 (mt) cc_final: 0.8461 (tt) REVERT: A 432 MET cc_start: 0.7989 (tpt) cc_final: 0.7461 (tpt) REVERT: A 435 ILE cc_start: 0.9106 (mt) cc_final: 0.8791 (tp) REVERT: A 470 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7509 (tpp80) REVERT: A 488 MET cc_start: 0.8109 (tpp) cc_final: 0.7898 (tpp) REVERT: A 496 LEU cc_start: 0.8940 (mm) cc_final: 0.8591 (tp) REVERT: A 519 ASN cc_start: 0.8234 (m110) cc_final: 0.7843 (m-40) REVERT: A 537 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8281 (ttmm) REVERT: A 543 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 556 TYR cc_start: 0.8693 (p90) cc_final: 0.8278 (p90) REVERT: A 563 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8701 (tppp) REVERT: A 578 TYR cc_start: 0.7440 (t80) cc_final: 0.6814 (t80) REVERT: A 580 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8445 (mmmt) REVERT: A 582 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 678 MET cc_start: 0.7245 (tmm) cc_final: 0.6844 (tmm) REVERT: A 681 LYS cc_start: 0.9048 (tptt) cc_final: 0.8475 (mmmm) REVERT: A 685 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8196 (mtm110) REVERT: A 687 ASP cc_start: 0.8415 (t0) cc_final: 0.8088 (t0) REVERT: A 694 LEU cc_start: 0.8723 (mm) cc_final: 0.8346 (mt) REVERT: A 701 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7974 (mm-30) REVERT: A 704 GLU cc_start: 0.8134 (tt0) cc_final: 0.7686 (tt0) REVERT: A 714 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7619 (mtt90) REVERT: A 732 GLN cc_start: 0.8427 (tt0) cc_final: 0.7578 (tm-30) REVERT: B 36 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7836 (mmt-90) REVERT: B 37 GLU cc_start: 0.7923 (pm20) cc_final: 0.7700 (pm20) REVERT: B 39 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7159 (mtp85) REVERT: B 46 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7165 (tm) REVERT: B 66 LYS cc_start: 0.8920 (tppt) cc_final: 0.8352 (tppt) REVERT: B 68 LEU cc_start: 0.8933 (tp) cc_final: 0.8667 (tp) REVERT: B 73 ASP cc_start: 0.7925 (t0) cc_final: 0.7696 (t0) REVERT: B 161 PHE cc_start: 0.7880 (m-80) cc_final: 0.7538 (m-10) REVERT: B 203 PHE cc_start: 0.8387 (m-80) cc_final: 0.7761 (m-80) REVERT: B 211 ILE cc_start: 0.8563 (tt) cc_final: 0.7966 (pt) REVERT: B 262 GLN cc_start: 0.8327 (tp40) cc_final: 0.8091 (tp-100) REVERT: B 264 ILE cc_start: 0.8788 (mm) cc_final: 0.8520 (mm) REVERT: B 273 ILE cc_start: 0.8695 (mt) cc_final: 0.8474 (pt) REVERT: B 282 CYS cc_start: 0.8716 (t) cc_final: 0.8466 (t) REVERT: B 291 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7515 (ttp-110) REVERT: B 292 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7172 (t80) REVERT: B 293 LYS cc_start: 0.8102 (tppt) cc_final: 0.7603 (tppt) REVERT: B 321 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7871 (tttt) REVERT: B 355 SER cc_start: 0.8994 (m) cc_final: 0.8706 (p) REVERT: B 369 LYS cc_start: 0.8748 (pttt) cc_final: 0.8268 (mmmt) REVERT: B 371 TYR cc_start: 0.7512 (m-80) cc_final: 0.6988 (m-80) REVERT: B 383 GLN cc_start: 0.8325 (tp40) cc_final: 0.7916 (tp40) REVERT: B 384 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 413 GLN cc_start: 0.8043 (pt0) cc_final: 0.7516 (pp30) REVERT: B 426 ILE cc_start: 0.8838 (mt) cc_final: 0.8499 (tp) REVERT: B 432 MET cc_start: 0.8089 (tpt) cc_final: 0.7617 (tpt) REVERT: B 435 ILE cc_start: 0.9073 (mt) cc_final: 0.8825 (tp) REVERT: B 447 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8475 (mtpp) REVERT: B 470 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7385 (tpp80) REVERT: B 473 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8539 (mppt) REVERT: B 475 ASN cc_start: 0.7142 (t0) cc_final: 0.6768 (t0) REVERT: B 486 CYS cc_start: 0.8962 (t) cc_final: 0.8686 (t) REVERT: B 496 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (mm) REVERT: B 503 LEU cc_start: 0.9008 (mt) cc_final: 0.8801 (mm) REVERT: B 507 LEU cc_start: 0.8561 (tp) cc_final: 0.8306 (tt) REVERT: B 512 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8329 (mtm180) REVERT: B 531 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8459 (mmmm) REVERT: B 537 LYS cc_start: 0.8614 (ttmm) cc_final: 0.7877 (mmtp) REVERT: B 580 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8332 (mmtm) REVERT: B 677 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7595 (ttm-80) REVERT: B 678 MET cc_start: 0.7443 (tpp) cc_final: 0.6834 (tpp) REVERT: B 681 LYS cc_start: 0.9022 (tptt) cc_final: 0.8453 (mmmm) REVERT: B 698 ASP cc_start: 0.7954 (t0) cc_final: 0.7651 (t70) REVERT: B 701 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 714 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7502 (mtt90) REVERT: B 732 GLN cc_start: 0.8179 (tt0) cc_final: 0.7612 (tm-30) outliers start: 49 outliers final: 34 residues processed: 359 average time/residue: 0.2607 time to fit residues: 126.0856 Evaluate side-chains 367 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 261 PHE 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 513 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS 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 89 ILE Chi-restraints excluded: chain B residue 100 LEU 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 350 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 433 VAL 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 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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** A 656 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.113996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096387 restraints weight = 23291.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099716 restraints weight = 11954.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101862 restraints weight = 7335.704| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10400 Z= 0.146 Angle : 0.667 10.826 14136 Z= 0.337 Chirality : 0.043 0.191 1718 Planarity : 0.004 0.036 1758 Dihedral : 5.188 51.142 1432 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1322 helix: 0.93 (0.18), residues: 830 sheet: -1.85 (0.88), residues: 36 loop : -1.99 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.019 0.003 HIS A 375 PHE 0.022 0.001 PHE A 354 TYR 0.020 0.001 TYR A 530 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 575) hydrogen bonds : angle 3.79192 ( 1683) covalent geometry : bond 0.00318 (10400) covalent geometry : angle 0.66696 (14136) *********************** 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 : 1.058 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: 0.8311 (m-10) cc_final: 0.8104 (m-10) REVERT: A 37 GLU cc_start: 0.8057 (pm20) cc_final: 0.7506 (pm20) REVERT: A 66 LYS cc_start: 0.8572 (mmmt) cc_final: 0.7938 (mmtm) REVERT: A 83 TRP cc_start: 0.6538 (m-10) cc_final: 0.6301 (m-10) REVERT: A 96 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8865 (mm) REVERT: A 121 PHE cc_start: 0.8334 (t80) cc_final: 0.7928 (t80) REVERT: A 122 PHE cc_start: 0.8252 (m-80) cc_final: 0.7745 (m-80) REVERT: A 145 SER cc_start: 0.8635 (m) cc_final: 0.8194 (p) REVERT: A 160 HIS cc_start: 0.7046 (t-90) cc_final: 0.6742 (t-90) REVERT: A 161 PHE cc_start: 0.7673 (m-80) cc_final: 0.7082 (m-80) REVERT: A 182 ASP cc_start: 0.8356 (m-30) cc_final: 0.8016 (m-30) REVERT: A 200 GLN cc_start: 0.8358 (tt0) cc_final: 0.7977 (tt0) REVERT: A 229 PHE cc_start: 0.8614 (t80) cc_final: 0.8337 (t80) REVERT: A 235 GLN cc_start: 0.8094 (mm110) cc_final: 0.7826 (mm-40) REVERT: A 238 ILE cc_start: 0.8771 (mt) cc_final: 0.8491 (mt) REVERT: A 242 VAL cc_start: 0.9037 (m) cc_final: 0.8699 (p) REVERT: A 258 ILE cc_start: 0.8840 (mm) cc_final: 0.8532 (tp) REVERT: A 283 MET cc_start: 0.7923 (tpp) cc_final: 0.7580 (mpp) REVERT: A 292 PHE cc_start: 0.7707 (t80) cc_final: 0.7305 (t80) REVERT: A 293 LYS cc_start: 0.8896 (tppt) cc_final: 0.8485 (tppt) REVERT: A 349 MET cc_start: 0.7079 (ptp) cc_final: 0.6860 (ptm) REVERT: A 361 TYR cc_start: 0.8668 (t80) cc_final: 0.8340 (t80) REVERT: A 384 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 385 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8586 (t80) REVERT: A 394 PHE cc_start: 0.8544 (t80) cc_final: 0.7509 (t80) REVERT: A 422 VAL cc_start: 0.8608 (t) cc_final: 0.8249 (m) REVERT: A 426 ILE cc_start: 0.8929 (mt) cc_final: 0.8461 (tt) REVERT: A 432 MET cc_start: 0.8007 (tpt) cc_final: 0.7479 (tpt) REVERT: A 435 ILE cc_start: 0.9116 (mt) cc_final: 0.8808 (tp) REVERT: A 470 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7593 (tpp80) REVERT: A 488 MET cc_start: 0.8026 (tpp) cc_final: 0.7785 (tpp) REVERT: A 496 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 519 ASN cc_start: 0.8253 (m110) cc_final: 0.7846 (m-40) REVERT: A 537 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8267 (ttmm) REVERT: A 543 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 556 TYR cc_start: 0.8708 (p90) cc_final: 0.8289 (p90) REVERT: A 563 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8717 (tppp) REVERT: A 578 TYR cc_start: 0.7453 (t80) cc_final: 0.6823 (t80) REVERT: A 579 ASN cc_start: 0.8343 (p0) cc_final: 0.7768 (p0) REVERT: A 580 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8605 (mmtm) REVERT: A 582 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8804 (mm) REVERT: A 678 MET cc_start: 0.7270 (tmm) cc_final: 0.6866 (tmm) REVERT: A 681 LYS cc_start: 0.9063 (tptt) cc_final: 0.8514 (mmmm) REVERT: A 685 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8180 (mtm110) REVERT: A 687 ASP cc_start: 0.8431 (t0) cc_final: 0.8115 (t0) REVERT: A 694 LEU cc_start: 0.8755 (mm) cc_final: 0.8374 (mt) REVERT: A 701 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 704 GLU cc_start: 0.8122 (tt0) cc_final: 0.7640 (tt0) REVERT: A 714 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7634 (mtt90) REVERT: A 732 GLN cc_start: 0.8461 (tt0) cc_final: 0.7590 (tm-30) REVERT: B 36 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7829 (mmt-90) REVERT: B 37 GLU cc_start: 0.7932 (pm20) cc_final: 0.7678 (pm20) REVERT: B 39 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7203 (mtp85) REVERT: B 46 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7162 (tm) REVERT: B 66 LYS cc_start: 0.8963 (tppt) cc_final: 0.8599 (tppt) REVERT: B 68 LEU cc_start: 0.8913 (tp) cc_final: 0.8646 (tp) REVERT: B 73 ASP cc_start: 0.7986 (t0) cc_final: 0.7656 (t0) REVERT: B 96 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 118 TYR cc_start: 0.8138 (m-10) cc_final: 0.7581 (m-80) REVERT: B 161 PHE cc_start: 0.7945 (m-80) cc_final: 0.7596 (m-10) REVERT: B 182 ASP cc_start: 0.7836 (p0) cc_final: 0.7532 (p0) REVERT: B 203 PHE cc_start: 0.8371 (m-80) cc_final: 0.7738 (m-80) REVERT: B 211 ILE cc_start: 0.8588 (tt) cc_final: 0.7987 (pt) REVERT: B 213 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7664 (mtm-85) REVERT: B 240 LEU cc_start: 0.9234 (mt) cc_final: 0.8827 (tt) REVERT: B 262 GLN cc_start: 0.8370 (tp40) cc_final: 0.8144 (tm-30) REVERT: B 264 ILE cc_start: 0.8845 (mm) cc_final: 0.8575 (mm) REVERT: B 271 ASP cc_start: 0.8000 (p0) cc_final: 0.7750 (p0) REVERT: B 273 ILE cc_start: 0.8746 (mt) cc_final: 0.8495 (pt) REVERT: B 282 CYS cc_start: 0.8714 (t) cc_final: 0.8452 (t) REVERT: B 291 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: B 292 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7072 (t80) REVERT: B 355 SER cc_start: 0.8974 (m) cc_final: 0.8681 (p) REVERT: B 369 LYS cc_start: 0.8758 (pttt) cc_final: 0.8412 (mmtm) REVERT: B 371 TYR cc_start: 0.7508 (m-80) cc_final: 0.7114 (m-80) REVERT: B 383 GLN cc_start: 0.8340 (tp40) cc_final: 0.7995 (tp40) REVERT: B 384 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 413 GLN cc_start: 0.8046 (pt0) cc_final: 0.7516 (tm-30) REVERT: B 426 ILE cc_start: 0.8864 (mt) cc_final: 0.8491 (tp) REVERT: B 432 MET cc_start: 0.8150 (tpt) cc_final: 0.7512 (tpt) REVERT: B 435 ILE cc_start: 0.9164 (mt) cc_final: 0.8860 (tp) REVERT: B 447 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8518 (mtpp) REVERT: B 470 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7449 (tpp80) REVERT: B 473 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8559 (mppt) REVERT: B 475 ASN cc_start: 0.7162 (t0) cc_final: 0.6783 (t0) REVERT: B 486 CYS cc_start: 0.8973 (t) cc_final: 0.8688 (t) REVERT: B 495 ASP cc_start: 0.8361 (p0) cc_final: 0.8010 (p0) REVERT: B 496 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8477 (mm) REVERT: B 503 LEU cc_start: 0.9030 (mt) cc_final: 0.8828 (mm) REVERT: B 507 LEU cc_start: 0.8599 (tp) cc_final: 0.8357 (tt) REVERT: B 512 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8331 (mtm180) REVERT: B 537 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8297 (ttmm) REVERT: B 556 TYR cc_start: 0.8726 (p90) cc_final: 0.8514 (p90) REVERT: B 580 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8349 (mmtm) REVERT: B 677 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7753 (tpp80) REVERT: B 681 LYS cc_start: 0.9059 (tptt) cc_final: 0.8499 (mmmm) REVERT: B 698 ASP cc_start: 0.7964 (t0) cc_final: 0.7624 (t70) REVERT: B 701 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 714 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7530 (mtt90) REVERT: B 732 GLN cc_start: 0.8462 (tt0) cc_final: 0.7537 (tm-30) outliers start: 53 outliers final: 37 residues processed: 364 average time/residue: 0.2820 time to fit residues: 137.7102 Evaluate side-chains 381 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 335 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 261 PHE 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 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 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 405 THR Chi-restraints excluded: chain B residue 433 VAL 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 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 413 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.112926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095291 restraints weight = 23394.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098600 restraints weight = 12029.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.100825 restraints weight = 7414.915| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10400 Z= 0.155 Angle : 0.674 10.003 14136 Z= 0.340 Chirality : 0.043 0.171 1718 Planarity : 0.004 0.050 1758 Dihedral : 5.123 51.069 1432 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.63 % Allowed : 18.81 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1322 helix: 0.92 (0.18), residues: 840 sheet: -2.41 (0.71), residues: 48 loop : -1.92 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 83 HIS 0.017 0.002 HIS A 375 PHE 0.036 0.002 PHE B 121 TYR 0.020 0.001 TYR A 530 ARG 0.005 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 575) hydrogen bonds : angle 3.78719 ( 1683) covalent geometry : bond 0.00335 (10400) covalent geometry : angle 0.67404 (14136) *********************** 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 390 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8057 (pm20) cc_final: 0.7485 (pm20) REVERT: A 66 LYS cc_start: 0.8596 (mmmt) cc_final: 0.7949 (mmtm) REVERT: A 83 TRP cc_start: 0.6561 (m-10) cc_final: 0.6274 (m-10) REVERT: A 96 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8853 (mm) REVERT: A 97 VAL cc_start: 0.9060 (t) cc_final: 0.8766 (p) REVERT: A 121 PHE cc_start: 0.8358 (t80) cc_final: 0.8064 (t80) REVERT: A 122 PHE cc_start: 0.8246 (m-80) cc_final: 0.7807 (m-80) REVERT: A 145 SER cc_start: 0.8648 (m) cc_final: 0.8212 (p) REVERT: A 160 HIS cc_start: 0.7091 (t-90) cc_final: 0.6787 (t-90) REVERT: A 161 PHE cc_start: 0.7706 (m-80) cc_final: 0.7136 (m-80) REVERT: A 182 ASP cc_start: 0.8331 (m-30) cc_final: 0.7795 (m-30) REVERT: A 200 GLN cc_start: 0.8383 (tt0) cc_final: 0.8015 (tt0) REVERT: A 229 PHE cc_start: 0.8622 (t80) cc_final: 0.8336 (t80) REVERT: A 235 GLN cc_start: 0.8104 (mm110) cc_final: 0.7824 (mm-40) REVERT: A 238 ILE cc_start: 0.8764 (mt) cc_final: 0.8491 (mt) REVERT: A 242 VAL cc_start: 0.9034 (m) cc_final: 0.8696 (p) REVERT: A 277 LEU cc_start: 0.8558 (tp) cc_final: 0.8266 (mm) REVERT: A 283 MET cc_start: 0.8236 (tpp) cc_final: 0.7308 (mmm) REVERT: A 286 LYS cc_start: 0.9192 (ptmt) cc_final: 0.8527 (pttp) REVERT: A 292 PHE cc_start: 0.7726 (t80) cc_final: 0.7297 (t80) REVERT: A 293 LYS cc_start: 0.8897 (tppt) cc_final: 0.8494 (tppt) REVERT: A 361 TYR cc_start: 0.8686 (t80) cc_final: 0.8466 (t80) REVERT: A 384 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 394 PHE cc_start: 0.8568 (t80) cc_final: 0.7680 (t80) REVERT: A 422 VAL cc_start: 0.8619 (t) cc_final: 0.8261 (m) REVERT: A 426 ILE cc_start: 0.8934 (mt) cc_final: 0.8471 (tt) REVERT: A 432 MET cc_start: 0.8026 (tpt) cc_final: 0.7602 (tpt) REVERT: A 435 ILE cc_start: 0.9128 (mt) cc_final: 0.8835 (tp) REVERT: A 464 GLN cc_start: 0.8639 (tt0) cc_final: 0.8006 (tp40) REVERT: A 467 ASP cc_start: 0.8267 (p0) cc_final: 0.7142 (p0) REVERT: A 470 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7611 (tpp80) REVERT: A 496 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8630 (mm) REVERT: A 514 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 519 ASN cc_start: 0.8252 (m110) cc_final: 0.7820 (m-40) REVERT: A 529 ILE cc_start: 0.8261 (tp) cc_final: 0.7990 (pt) REVERT: A 537 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8253 (ttmm) REVERT: A 543 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 556 TYR cc_start: 0.8758 (p90) cc_final: 0.8408 (p90) REVERT: A 563 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8706 (tppp) REVERT: A 578 TYR cc_start: 0.7471 (t80) cc_final: 0.6942 (t80) REVERT: A 579 ASN cc_start: 0.8336 (p0) cc_final: 0.7720 (p0) REVERT: A 580 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8604 (mmtm) REVERT: A 678 MET cc_start: 0.7280 (tmm) cc_final: 0.6923 (tmm) REVERT: A 681 LYS cc_start: 0.9069 (tptt) cc_final: 0.8530 (mmmm) REVERT: A 685 ARG cc_start: 0.8494 (mtm180) cc_final: 0.8126 (mtm110) REVERT: A 687 ASP cc_start: 0.8461 (t0) cc_final: 0.8126 (t0) REVERT: A 694 LEU cc_start: 0.8808 (mm) cc_final: 0.8392 (mt) REVERT: A 698 ASP cc_start: 0.7716 (t0) cc_final: 0.7468 (t0) REVERT: A 701 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 714 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7630 (mtt90) REVERT: A 732 GLN cc_start: 0.8468 (tt0) cc_final: 0.7655 (tm-30) REVERT: B 36 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7809 (mmt-90) REVERT: B 37 GLU cc_start: 0.7901 (pm20) cc_final: 0.7651 (pm20) REVERT: B 39 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7225 (mtp85) REVERT: B 46 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7160 (tm) REVERT: B 66 LYS cc_start: 0.8903 (tppt) cc_final: 0.8567 (tppt) REVERT: B 68 LEU cc_start: 0.8936 (tp) cc_final: 0.8665 (tp) REVERT: B 73 ASP cc_start: 0.7948 (t0) cc_final: 0.7571 (t0) REVERT: B 118 TYR cc_start: 0.8150 (m-10) cc_final: 0.7595 (m-80) REVERT: B 161 PHE cc_start: 0.7946 (m-80) cc_final: 0.7678 (m-10) REVERT: B 203 PHE cc_start: 0.8339 (m-80) cc_final: 0.7762 (m-80) REVERT: B 211 ILE cc_start: 0.8640 (tt) cc_final: 0.8040 (pt) REVERT: B 213 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7599 (mtm-85) REVERT: B 240 LEU cc_start: 0.9249 (mt) cc_final: 0.8846 (tt) REVERT: B 262 GLN cc_start: 0.8370 (tp40) cc_final: 0.8116 (tm-30) REVERT: B 264 ILE cc_start: 0.8878 (mm) cc_final: 0.8606 (mm) REVERT: B 273 ILE cc_start: 0.8754 (mt) cc_final: 0.8500 (pt) REVERT: B 282 CYS cc_start: 0.8726 (t) cc_final: 0.8208 (t) REVERT: B 283 MET cc_start: 0.8049 (tpp) cc_final: 0.7558 (tpp) REVERT: B 286 LYS cc_start: 0.8940 (tppt) cc_final: 0.8595 (ptmm) REVERT: B 287 GLU cc_start: 0.8514 (tp30) cc_final: 0.7689 (tp30) REVERT: B 292 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7117 (t80) REVERT: B 355 SER cc_start: 0.8925 (m) cc_final: 0.8634 (p) REVERT: B 369 LYS cc_start: 0.8752 (pttt) cc_final: 0.8494 (mtmt) REVERT: B 371 TYR cc_start: 0.7373 (m-80) cc_final: 0.7134 (m-80) REVERT: B 383 GLN cc_start: 0.8327 (tp40) cc_final: 0.7989 (tp40) REVERT: B 384 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 413 GLN cc_start: 0.8097 (pt0) cc_final: 0.7583 (tm-30) REVERT: B 421 GLN cc_start: 0.8115 (mm110) cc_final: 0.7826 (mm110) REVERT: B 426 ILE cc_start: 0.8848 (mt) cc_final: 0.8498 (tp) REVERT: B 432 MET cc_start: 0.8075 (tpt) cc_final: 0.7599 (tpt) REVERT: B 435 ILE cc_start: 0.9167 (mt) cc_final: 0.8859 (tp) REVERT: B 447 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8593 (mtpp) REVERT: B 470 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7462 (tpp80) REVERT: B 473 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8568 (mppt) REVERT: B 475 ASN cc_start: 0.7175 (t0) cc_final: 0.6791 (t0) REVERT: B 486 CYS cc_start: 0.8968 (t) cc_final: 0.8682 (t) REVERT: B 495 ASP cc_start: 0.8389 (p0) cc_final: 0.8040 (p0) REVERT: B 496 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8473 (mm) REVERT: B 507 LEU cc_start: 0.8641 (tp) cc_final: 0.8393 (tt) REVERT: B 512 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (mtm180) REVERT: B 537 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8254 (ttmm) REVERT: B 546 LYS cc_start: 0.8127 (tppt) cc_final: 0.7647 (tppt) REVERT: B 556 TYR cc_start: 0.8760 (p90) cc_final: 0.8555 (p90) REVERT: B 580 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8359 (mmtm) REVERT: B 677 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7598 (ttm-80) REVERT: B 681 LYS cc_start: 0.9062 (tptt) cc_final: 0.8519 (mmmm) REVERT: B 682 GLU cc_start: 0.7935 (tp30) cc_final: 0.7565 (tp30) REVERT: B 698 ASP cc_start: 0.8078 (t0) cc_final: 0.7561 (t0) REVERT: B 701 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 714 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7552 (mtt90) REVERT: B 732 GLN cc_start: 0.8412 (tt0) cc_final: 0.7511 (tm-30) outliers start: 52 outliers final: 43 residues processed: 364 average time/residue: 0.2467 time to fit residues: 120.0152 Evaluate side-chains 385 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 261 PHE 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 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 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 405 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5142 ------------------------------------------------------------------------------- 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 413 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095284 restraints weight = 23410.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098604 restraints weight = 11882.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100698 restraints weight = 7225.892| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10400 Z= 0.152 Angle : 0.693 11.271 14136 Z= 0.351 Chirality : 0.043 0.163 1718 Planarity : 0.004 0.047 1758 Dihedral : 5.110 50.792 1432 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.81 % Allowed : 19.34 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1322 helix: 1.04 (0.18), residues: 828 sheet: -1.58 (0.89), residues: 36 loop : -1.90 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 83 HIS 0.017 0.003 HIS A 728 PHE 0.022 0.001 PHE A 354 TYR 0.043 0.002 TYR B 105 ARG 0.009 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 575) hydrogen bonds : angle 3.84395 ( 1683) covalent geometry : bond 0.00333 (10400) covalent geometry : angle 0.69276 (14136) *********************** 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 397 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 1.129 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 37 GLU cc_start: 0.8056 (pm20) cc_final: 0.7569 (pm20) REVERT: A 39 ARG cc_start: 0.7610 (ttm110) cc_final: 0.6830 (mtp85) REVERT: A 66 LYS cc_start: 0.8599 (mmmt) cc_final: 0.7968 (mmtm) REVERT: A 83 TRP cc_start: 0.6585 (m-10) cc_final: 0.6334 (m-10) REVERT: A 96 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 97 VAL cc_start: 0.9041 (t) cc_final: 0.8753 (p) REVERT: A 121 PHE cc_start: 0.8354 (t80) cc_final: 0.8064 (t80) REVERT: A 122 PHE cc_start: 0.8245 (m-80) cc_final: 0.7802 (m-80) REVERT: A 145 SER cc_start: 0.8645 (m) cc_final: 0.8218 (p) REVERT: A 160 HIS cc_start: 0.7112 (t-90) cc_final: 0.6804 (t-90) REVERT: A 161 PHE cc_start: 0.7710 (m-80) cc_final: 0.7136 (m-80) REVERT: A 200 GLN cc_start: 0.8353 (tt0) cc_final: 0.8001 (tt0) REVERT: A 235 GLN cc_start: 0.8077 (mm110) cc_final: 0.7810 (mm-40) REVERT: A 238 ILE cc_start: 0.8767 (mt) cc_final: 0.8493 (mt) REVERT: A 242 VAL cc_start: 0.9021 (m) cc_final: 0.8686 (p) REVERT: A 277 LEU cc_start: 0.8550 (tp) cc_final: 0.8260 (mm) REVERT: A 283 MET cc_start: 0.8174 (tpp) cc_final: 0.7200 (mpp) REVERT: A 286 LYS cc_start: 0.9161 (ptmt) cc_final: 0.8579 (pttp) REVERT: A 292 PHE cc_start: 0.7782 (t80) cc_final: 0.7347 (t80) REVERT: A 293 LYS cc_start: 0.8905 (tppt) cc_final: 0.8485 (tppt) REVERT: A 361 TYR cc_start: 0.8681 (t80) cc_final: 0.8424 (t80) REVERT: A 384 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 394 PHE cc_start: 0.8559 (t80) cc_final: 0.7673 (t80) REVERT: A 422 VAL cc_start: 0.8613 (t) cc_final: 0.8257 (m) REVERT: A 426 ILE cc_start: 0.8936 (mt) cc_final: 0.8474 (tt) REVERT: A 432 MET cc_start: 0.7999 (tpt) cc_final: 0.7583 (tpt) REVERT: A 435 ILE cc_start: 0.9131 (mt) cc_final: 0.8838 (tp) REVERT: A 464 GLN cc_start: 0.8638 (tt0) cc_final: 0.7982 (tp40) REVERT: A 467 ASP cc_start: 0.8232 (p0) cc_final: 0.7044 (p0) REVERT: A 470 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7597 (tpp80) REVERT: A 473 LYS cc_start: 0.8919 (mptt) cc_final: 0.8539 (mppt) REVERT: A 488 MET cc_start: 0.8141 (tpp) cc_final: 0.7874 (tpp) REVERT: A 496 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8623 (mm) REVERT: A 519 ASN cc_start: 0.8230 (m110) cc_final: 0.7729 (m-40) REVERT: A 537 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8255 (ttmm) REVERT: A 543 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 556 TYR cc_start: 0.8746 (p90) cc_final: 0.8389 (p90) REVERT: A 563 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8705 (tppp) REVERT: A 578 TYR cc_start: 0.7445 (t80) cc_final: 0.6961 (t80) REVERT: A 579 ASN cc_start: 0.8309 (p0) cc_final: 0.7774 (p0) REVERT: A 580 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8442 (mmtm) REVERT: A 583 LYS cc_start: 0.8955 (pptt) cc_final: 0.8569 (ptpt) REVERT: A 678 MET cc_start: 0.7352 (tmm) cc_final: 0.6979 (tmm) REVERT: A 681 LYS cc_start: 0.9070 (tptt) cc_final: 0.8536 (mmmm) REVERT: A 685 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8173 (mtm180) REVERT: A 687 ASP cc_start: 0.8464 (t0) cc_final: 0.7968 (t0) REVERT: A 694 LEU cc_start: 0.8781 (mm) cc_final: 0.8343 (mt) REVERT: A 698 ASP cc_start: 0.7724 (t0) cc_final: 0.7493 (t0) REVERT: A 701 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 714 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7613 (mtt90) REVERT: A 732 GLN cc_start: 0.8483 (tt0) cc_final: 0.7676 (tm-30) REVERT: B 36 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7812 (mmt-90) REVERT: B 37 GLU cc_start: 0.7887 (pm20) cc_final: 0.7651 (pm20) REVERT: B 39 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7243 (mtp85) REVERT: B 46 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7158 (tm) REVERT: B 66 LYS cc_start: 0.8870 (tppt) cc_final: 0.8518 (tppt) REVERT: B 68 LEU cc_start: 0.8937 (tp) cc_final: 0.8661 (tp) REVERT: B 73 ASP cc_start: 0.7925 (t0) cc_final: 0.7524 (t0) REVERT: B 101 GLN cc_start: 0.8460 (tt0) cc_final: 0.8092 (tt0) REVERT: B 105 TYR cc_start: 0.8658 (m-80) cc_final: 0.8233 (m-80) REVERT: B 118 TYR cc_start: 0.8143 (m-10) cc_final: 0.7584 (m-80) REVERT: B 132 THR cc_start: 0.7912 (t) cc_final: 0.6242 (t) REVERT: B 161 PHE cc_start: 0.7970 (m-80) cc_final: 0.7721 (m-10) REVERT: B 193 THR cc_start: 0.8922 (m) cc_final: 0.8587 (p) REVERT: B 203 PHE cc_start: 0.8325 (m-80) cc_final: 0.7813 (m-80) REVERT: B 211 ILE cc_start: 0.8615 (tt) cc_final: 0.8083 (pt) REVERT: B 213 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7300 (mtm-85) REVERT: B 240 LEU cc_start: 0.9250 (mt) cc_final: 0.8790 (tt) REVERT: B 262 GLN cc_start: 0.8371 (tp40) cc_final: 0.8094 (tm-30) REVERT: B 264 ILE cc_start: 0.8899 (mm) cc_final: 0.8620 (mm) REVERT: B 273 ILE cc_start: 0.8759 (mt) cc_final: 0.8511 (pt) REVERT: B 282 CYS cc_start: 0.8677 (t) cc_final: 0.8180 (t) REVERT: B 283 MET cc_start: 0.7963 (tpp) cc_final: 0.7517 (tpp) REVERT: B 286 LYS cc_start: 0.8925 (tppt) cc_final: 0.8596 (ptmm) REVERT: B 287 GLU cc_start: 0.8480 (tp30) cc_final: 0.7661 (tp30) REVERT: B 292 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7052 (t80) REVERT: B 355 SER cc_start: 0.8929 (m) cc_final: 0.8650 (p) REVERT: B 369 LYS cc_start: 0.8735 (pttt) cc_final: 0.8455 (mtmt) REVERT: B 371 TYR cc_start: 0.7336 (m-80) cc_final: 0.7102 (m-80) REVERT: B 383 GLN cc_start: 0.8299 (tp40) cc_final: 0.8017 (tp40) REVERT: B 384 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 413 GLN cc_start: 0.8023 (pt0) cc_final: 0.7600 (tm-30) REVERT: B 426 ILE cc_start: 0.8849 (mt) cc_final: 0.8499 (tp) REVERT: B 432 MET cc_start: 0.8097 (tpt) cc_final: 0.7566 (tpt) REVERT: B 435 ILE cc_start: 0.9162 (mt) cc_final: 0.8848 (tp) REVERT: B 447 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8661 (mtpp) REVERT: B 470 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7459 (tpp80) REVERT: B 473 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8560 (mppt) REVERT: B 475 ASN cc_start: 0.7184 (t0) cc_final: 0.6807 (t0) REVERT: B 486 CYS cc_start: 0.8946 (t) cc_final: 0.8688 (t) REVERT: B 495 ASP cc_start: 0.8370 (p0) cc_final: 0.7987 (p0) REVERT: B 496 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 507 LEU cc_start: 0.8628 (tp) cc_final: 0.8389 (tt) REVERT: B 512 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8249 (mtm180) REVERT: B 514 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 537 LYS cc_start: 0.8598 (ttmm) cc_final: 0.7992 (mmtm) REVERT: B 546 LYS cc_start: 0.8106 (tppt) cc_final: 0.7560 (tppt) REVERT: B 556 TYR cc_start: 0.8726 (p90) cc_final: 0.8495 (p90) REVERT: B 580 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8358 (mmtm) REVERT: B 668 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7523 (tp) REVERT: B 677 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7608 (ttm-80) REVERT: B 681 LYS cc_start: 0.9060 (tptt) cc_final: 0.8497 (mmmm) REVERT: B 697 ASP cc_start: 0.8048 (m-30) cc_final: 0.7775 (m-30) REVERT: B 698 ASP cc_start: 0.7999 (t0) cc_final: 0.7624 (t70) REVERT: B 701 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 714 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7548 (mtt90) REVERT: B 724 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 732 GLN cc_start: 0.8363 (tt0) cc_final: 0.7525 (tm-30) outliers start: 54 outliers final: 41 residues processed: 371 average time/residue: 0.2584 time to fit residues: 128.3622 Evaluate side-chains 394 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 261 PHE 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 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 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 422 VAL Chi-restraints excluded: chain B residue 433 VAL 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 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 Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 108 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN ** A 519 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.113438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095737 restraints weight = 23494.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099083 restraints weight = 11979.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.101246 restraints weight = 7291.328| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10400 Z= 0.151 Angle : 0.721 15.038 14136 Z= 0.360 Chirality : 0.044 0.253 1718 Planarity : 0.004 0.044 1758 Dihedral : 5.132 50.606 1430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.72 % Allowed : 20.68 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.24), residues: 1322 helix: 1.05 (0.18), residues: 828 sheet: -1.39 (0.91), residues: 36 loop : -1.86 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 83 HIS 0.021 0.003 HIS B 375 PHE 0.024 0.001 PHE B 394 TYR 0.037 0.002 TYR B 105 ARG 0.007 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 575) hydrogen bonds : angle 3.84588 ( 1683) covalent geometry : bond 0.00335 (10400) covalent geometry : angle 0.72074 (14136) *********************** 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 406 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 1.073 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: A 39 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7364 (ttm110) REVERT: A 66 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8079 (mmtm) REVERT: A 83 TRP cc_start: 0.6559 (m-10) cc_final: 0.6318 (m-10) REVERT: A 96 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 97 VAL cc_start: 0.9039 (t) cc_final: 0.8756 (p) REVERT: A 122 PHE cc_start: 0.8237 (m-80) cc_final: 0.7753 (m-80) REVERT: A 145 SER cc_start: 0.8667 (m) cc_final: 0.8256 (p) REVERT: A 160 HIS cc_start: 0.7105 (t-90) cc_final: 0.6772 (t-90) REVERT: A 161 PHE cc_start: 0.7671 (m-80) cc_final: 0.7088 (m-80) REVERT: A 193 THR cc_start: 0.8745 (m) cc_final: 0.8422 (p) REVERT: A 200 GLN cc_start: 0.8343 (tt0) cc_final: 0.8002 (tt0) REVERT: A 229 PHE cc_start: 0.8610 (t80) cc_final: 0.8394 (t80) REVERT: A 235 GLN cc_start: 0.8076 (mm110) cc_final: 0.7802 (mm-40) REVERT: A 238 ILE cc_start: 0.8752 (mt) cc_final: 0.8477 (mt) REVERT: A 242 VAL cc_start: 0.9025 (m) cc_final: 0.8689 (p) REVERT: A 258 ILE cc_start: 0.8956 (tp) cc_final: 0.8568 (pt) REVERT: A 277 LEU cc_start: 0.8571 (tp) cc_final: 0.8289 (mm) REVERT: A 286 LYS cc_start: 0.9159 (ptmt) cc_final: 0.8555 (pttp) REVERT: A 292 PHE cc_start: 0.7782 (t80) cc_final: 0.7340 (t80) REVERT: A 293 LYS cc_start: 0.8916 (tppt) cc_final: 0.8493 (tppt) REVERT: A 361 TYR cc_start: 0.8689 (t80) cc_final: 0.8434 (t80) REVERT: A 384 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 394 PHE cc_start: 0.8559 (t80) cc_final: 0.7527 (t80) REVERT: A 422 VAL cc_start: 0.8602 (t) cc_final: 0.8243 (m) REVERT: A 426 ILE cc_start: 0.8935 (mt) cc_final: 0.8474 (tt) REVERT: A 432 MET cc_start: 0.7987 (tpt) cc_final: 0.7547 (tpt) REVERT: A 435 ILE cc_start: 0.9131 (mt) cc_final: 0.8846 (tp) REVERT: A 464 GLN cc_start: 0.8636 (tt0) cc_final: 0.7961 (tp40) REVERT: A 467 ASP cc_start: 0.8213 (p0) cc_final: 0.7003 (p0) REVERT: A 470 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7602 (tpp80) REVERT: A 472 TRP cc_start: 0.8872 (t-100) cc_final: 0.8538 (t-100) REVERT: A 473 LYS cc_start: 0.8926 (mptt) cc_final: 0.8542 (mppt) REVERT: A 476 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8733 (mmtm) REVERT: A 488 MET cc_start: 0.8127 (tpp) cc_final: 0.7869 (tpp) REVERT: A 496 LEU cc_start: 0.9014 (mm) cc_final: 0.8657 (mm) REVERT: A 514 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A 519 ASN cc_start: 0.8253 (m110) cc_final: 0.7724 (m-40) REVERT: A 537 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8225 (ttmm) REVERT: A 543 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 545 VAL cc_start: 0.8743 (t) cc_final: 0.8187 (p) REVERT: A 556 TYR cc_start: 0.8746 (p90) cc_final: 0.8395 (p90) REVERT: A 563 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8700 (tppp) REVERT: A 578 TYR cc_start: 0.7478 (t80) cc_final: 0.6664 (t80) REVERT: A 579 ASN cc_start: 0.8277 (p0) cc_final: 0.7497 (p0) REVERT: A 580 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8474 (mmtm) REVERT: A 583 LYS cc_start: 0.8964 (pptt) cc_final: 0.8563 (ptpt) REVERT: A 678 MET cc_start: 0.7357 (tmm) cc_final: 0.6978 (tmm) REVERT: A 681 LYS cc_start: 0.9069 (tptt) cc_final: 0.8539 (mmmm) REVERT: A 685 ARG cc_start: 0.8463 (mtm180) cc_final: 0.8164 (mtm110) REVERT: A 687 ASP cc_start: 0.8460 (t0) cc_final: 0.8121 (t0) REVERT: A 694 LEU cc_start: 0.8748 (mm) cc_final: 0.8302 (mt) REVERT: A 698 ASP cc_start: 0.7782 (t0) cc_final: 0.7539 (t0) REVERT: A 701 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 714 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7599 (mtt90) REVERT: A 732 GLN cc_start: 0.8488 (tt0) cc_final: 0.7559 (tm-30) REVERT: B 29 GLU cc_start: 0.8651 (tp30) cc_final: 0.8347 (tp30) REVERT: B 36 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7813 (mmt-90) REVERT: B 37 GLU cc_start: 0.7901 (pm20) cc_final: 0.7654 (pm20) REVERT: B 39 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7275 (mtp85) REVERT: B 46 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7166 (tm) REVERT: B 68 LEU cc_start: 0.8936 (tp) cc_final: 0.8662 (tp) REVERT: B 73 ASP cc_start: 0.7935 (t0) cc_final: 0.7605 (t0) REVERT: B 101 GLN cc_start: 0.8474 (tt0) cc_final: 0.8050 (tt0) REVERT: B 105 TYR cc_start: 0.8656 (m-80) cc_final: 0.8194 (m-80) REVERT: B 118 TYR cc_start: 0.8140 (m-10) cc_final: 0.7588 (m-80) REVERT: B 132 THR cc_start: 0.7902 (t) cc_final: 0.6253 (t) REVERT: B 193 THR cc_start: 0.8823 (m) cc_final: 0.8479 (p) REVERT: B 203 PHE cc_start: 0.8314 (m-80) cc_final: 0.7774 (m-80) REVERT: B 211 ILE cc_start: 0.8610 (tt) cc_final: 0.8114 (pt) REVERT: B 240 LEU cc_start: 0.9243 (mt) cc_final: 0.8782 (tt) REVERT: B 262 GLN cc_start: 0.8382 (tp40) cc_final: 0.8085 (tm-30) REVERT: B 264 ILE cc_start: 0.8889 (mm) cc_final: 0.8625 (mm) REVERT: B 266 ASP cc_start: 0.7843 (m-30) cc_final: 0.7470 (p0) REVERT: B 273 ILE cc_start: 0.8777 (mt) cc_final: 0.8517 (pt) REVERT: B 282 CYS cc_start: 0.8739 (t) cc_final: 0.8234 (t) REVERT: B 283 MET cc_start: 0.7979 (tpp) cc_final: 0.7525 (tpp) REVERT: B 286 LYS cc_start: 0.8936 (tppt) cc_final: 0.8572 (ptmm) REVERT: B 287 GLU cc_start: 0.8484 (tp30) cc_final: 0.7652 (tp30) REVERT: B 292 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7073 (t80) REVERT: B 355 SER cc_start: 0.8926 (m) cc_final: 0.8638 (p) REVERT: B 369 LYS cc_start: 0.8729 (pttt) cc_final: 0.8442 (mtmt) REVERT: B 371 TYR cc_start: 0.7288 (m-80) cc_final: 0.7061 (m-80) REVERT: B 383 GLN cc_start: 0.8315 (tp40) cc_final: 0.8050 (tp40) REVERT: B 384 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 413 GLN cc_start: 0.8026 (pt0) cc_final: 0.7590 (tm-30) REVERT: B 426 ILE cc_start: 0.8846 (mt) cc_final: 0.8493 (tp) REVERT: B 432 MET cc_start: 0.8115 (tpt) cc_final: 0.7584 (tpt) REVERT: B 435 ILE cc_start: 0.9166 (mt) cc_final: 0.8848 (tp) REVERT: B 447 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8622 (mtpp) REVERT: B 470 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7445 (tpp80) REVERT: B 473 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8559 (mppt) REVERT: B 475 ASN cc_start: 0.7169 (t0) cc_final: 0.5600 (t0) REVERT: B 478 ASP cc_start: 0.7956 (m-30) cc_final: 0.7219 (m-30) REVERT: B 486 CYS cc_start: 0.8915 (t) cc_final: 0.8661 (t) REVERT: B 496 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8574 (mm) REVERT: B 507 LEU cc_start: 0.8629 (tp) cc_final: 0.8373 (tt) REVERT: B 512 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8264 (mtm180) REVERT: B 514 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 528 ASP cc_start: 0.8142 (p0) cc_final: 0.7654 (p0) REVERT: B 556 TYR cc_start: 0.8729 (p90) cc_final: 0.8495 (p90) REVERT: B 580 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8351 (mmtm) REVERT: B 668 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7771 (tp) REVERT: B 669 ASP cc_start: 0.7309 (t0) cc_final: 0.6951 (t0) REVERT: B 677 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7574 (ttm-80) REVERT: B 681 LYS cc_start: 0.8977 (tptt) cc_final: 0.8579 (tppt) REVERT: B 691 TYR cc_start: 0.8190 (m-10) cc_final: 0.7844 (m-10) REVERT: B 697 ASP cc_start: 0.8041 (m-30) cc_final: 0.7769 (m-30) REVERT: B 698 ASP cc_start: 0.7972 (t0) cc_final: 0.7511 (t0) REVERT: B 701 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 714 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7595 (mtt90) REVERT: B 732 GLN cc_start: 0.8330 (tt0) cc_final: 0.7582 (tm-30) outliers start: 53 outliers final: 36 residues processed: 381 average time/residue: 0.2851 time to fit residues: 147.2629 Evaluate side-chains 386 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 344 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 261 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET 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 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 422 VAL Chi-restraints excluded: chain B residue 433 VAL 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 582 LEU Chi-restraints excluded: chain B residue 668 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 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 375 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.110789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093402 restraints weight = 23420.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096686 restraints weight = 11997.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098846 restraints weight = 7314.372| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10400 Z= 0.193 Angle : 0.779 16.480 14136 Z= 0.392 Chirality : 0.046 0.242 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.255 51.561 1429 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.10 % Allowed : 21.48 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1322 helix: 1.04 (0.18), residues: 830 sheet: -1.24 (0.92), residues: 36 loop : -1.90 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.018 0.002 HIS A 728 PHE 0.019 0.001 PHE A 354 TYR 0.035 0.002 TYR B 105 ARG 0.008 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 575) hydrogen bonds : angle 3.90523 ( 1683) covalent geometry : bond 0.00413 (10400) covalent geometry : angle 0.77895 (14136) ********************** 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 406 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7405 (ttm110) REVERT: A 83 TRP cc_start: 0.6605 (m-10) cc_final: 0.6322 (m-10) REVERT: A 96 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 97 VAL cc_start: 0.9071 (t) cc_final: 0.8804 (p) REVERT: A 122 PHE cc_start: 0.8218 (m-80) cc_final: 0.7833 (m-80) REVERT: A 145 SER cc_start: 0.8762 (m) cc_final: 0.8324 (p) REVERT: A 160 HIS cc_start: 0.7132 (t-90) cc_final: 0.6816 (t-90) REVERT: A 161 PHE cc_start: 0.7693 (m-80) cc_final: 0.7180 (m-80) REVERT: A 188 LEU cc_start: 0.9054 (tp) cc_final: 0.8808 (tp) REVERT: A 193 THR cc_start: 0.8764 (m) cc_final: 0.8450 (p) REVERT: A 200 GLN cc_start: 0.8352 (tt0) cc_final: 0.8017 (tt0) REVERT: A 213 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7735 (ptp-170) REVERT: A 238 ILE cc_start: 0.8773 (mt) cc_final: 0.8556 (mt) REVERT: A 242 VAL cc_start: 0.9023 (m) cc_final: 0.8719 (p) REVERT: A 277 LEU cc_start: 0.8630 (tp) cc_final: 0.8344 (mm) REVERT: A 286 LYS cc_start: 0.9131 (ptmt) cc_final: 0.8457 (pttp) REVERT: A 292 PHE cc_start: 0.7762 (t80) cc_final: 0.7301 (t80) REVERT: A 293 LYS cc_start: 0.8919 (tppt) cc_final: 0.8502 (tppt) REVERT: A 361 TYR cc_start: 0.8702 (t80) cc_final: 0.8473 (t80) REVERT: A 384 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 394 PHE cc_start: 0.8580 (t80) cc_final: 0.7585 (t80) REVERT: A 421 GLN cc_start: 0.8256 (mm-40) cc_final: 0.8028 (mm-40) REVERT: A 426 ILE cc_start: 0.8957 (mt) cc_final: 0.8477 (tt) REVERT: A 432 MET cc_start: 0.8036 (tpt) cc_final: 0.7608 (tpt) REVERT: A 435 ILE cc_start: 0.9157 (mt) cc_final: 0.8921 (tp) REVERT: A 470 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7655 (tpp80) REVERT: A 473 LYS cc_start: 0.8937 (mptt) cc_final: 0.8568 (mppt) REVERT: A 476 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8734 (mmtm) REVERT: A 488 MET cc_start: 0.8140 (tpp) cc_final: 0.7868 (tpp) REVERT: A 496 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 514 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 537 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8214 (ttmm) REVERT: A 541 GLU cc_start: 0.7835 (tp30) cc_final: 0.7629 (tp30) REVERT: A 543 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 545 VAL cc_start: 0.8672 (t) cc_final: 0.7959 (p) REVERT: A 556 TYR cc_start: 0.8813 (p90) cc_final: 0.8561 (p90) REVERT: A 563 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8687 (tppp) REVERT: A 578 TYR cc_start: 0.7510 (t80) cc_final: 0.6830 (t80) REVERT: A 579 ASN cc_start: 0.8273 (p0) cc_final: 0.7672 (p0) REVERT: A 580 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8636 (mmtm) REVERT: A 678 MET cc_start: 0.7348 (tmm) cc_final: 0.6999 (tmm) REVERT: A 681 LYS cc_start: 0.9095 (tptt) cc_final: 0.8584 (mmmm) REVERT: A 685 ARG cc_start: 0.8481 (mtm180) cc_final: 0.8210 (mtm110) REVERT: A 687 ASP cc_start: 0.8481 (t0) cc_final: 0.8121 (t0) REVERT: A 694 LEU cc_start: 0.8787 (mm) cc_final: 0.8400 (mt) REVERT: A 698 ASP cc_start: 0.7842 (t0) cc_final: 0.7581 (t0) REVERT: A 701 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 714 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7617 (mtt90) REVERT: A 732 GLN cc_start: 0.8533 (tt0) cc_final: 0.7647 (tm-30) REVERT: B 29 GLU cc_start: 0.8688 (tp30) cc_final: 0.8400 (tp30) REVERT: B 36 ARG cc_start: 0.8187 (tpp-160) cc_final: 0.7834 (mmt-90) REVERT: B 37 GLU cc_start: 0.7900 (pm20) cc_final: 0.7652 (pm20) REVERT: B 46 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7158 (tm) REVERT: B 68 LEU cc_start: 0.8939 (tp) cc_final: 0.8674 (tp) REVERT: B 73 ASP cc_start: 0.7938 (t0) cc_final: 0.7597 (t0) REVERT: B 101 GLN cc_start: 0.8476 (tt0) cc_final: 0.8019 (tt0) REVERT: B 105 TYR cc_start: 0.8683 (m-80) cc_final: 0.8179 (m-80) REVERT: B 118 TYR cc_start: 0.8159 (m-10) cc_final: 0.7429 (m-80) REVERT: B 130 PHE cc_start: 0.8231 (m-80) cc_final: 0.7890 (m-80) REVERT: B 193 THR cc_start: 0.8819 (m) cc_final: 0.8429 (p) REVERT: B 203 PHE cc_start: 0.8327 (m-80) cc_final: 0.7773 (m-80) REVERT: B 211 ILE cc_start: 0.8673 (tt) cc_final: 0.8132 (pt) REVERT: B 213 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7590 (mtm-85) REVERT: B 240 LEU cc_start: 0.9242 (mt) cc_final: 0.8823 (tt) REVERT: B 262 GLN cc_start: 0.8399 (tp40) cc_final: 0.8071 (tp-100) REVERT: B 264 ILE cc_start: 0.8944 (mm) cc_final: 0.8671 (mm) REVERT: B 266 ASP cc_start: 0.7968 (m-30) cc_final: 0.7374 (p0) REVERT: B 273 ILE cc_start: 0.8863 (mt) cc_final: 0.8562 (pt) REVERT: B 282 CYS cc_start: 0.8754 (t) cc_final: 0.8257 (t) REVERT: B 283 MET cc_start: 0.7947 (tpp) cc_final: 0.7512 (tpp) REVERT: B 286 LYS cc_start: 0.8945 (tppt) cc_final: 0.8592 (ptmm) REVERT: B 287 GLU cc_start: 0.8478 (tp30) cc_final: 0.7650 (tp30) REVERT: B 292 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 369 LYS cc_start: 0.8737 (pttt) cc_final: 0.8507 (mtmt) REVERT: B 383 GLN cc_start: 0.8327 (tp40) cc_final: 0.8016 (tp40) REVERT: B 384 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 413 GLN cc_start: 0.8043 (pt0) cc_final: 0.7583 (tm-30) REVERT: B 421 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7885 (mm110) REVERT: B 426 ILE cc_start: 0.8867 (mt) cc_final: 0.8510 (tp) REVERT: B 432 MET cc_start: 0.8151 (tpt) cc_final: 0.7527 (tpt) REVERT: B 435 ILE cc_start: 0.9179 (mt) cc_final: 0.8873 (tp) REVERT: B 447 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8628 (mtpp) REVERT: B 464 GLN cc_start: 0.8808 (tt0) cc_final: 0.7869 (tp-100) REVERT: B 470 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7449 (tpp80) REVERT: B 473 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8552 (mppt) REVERT: B 475 ASN cc_start: 0.7205 (t0) cc_final: 0.5679 (t0) REVERT: B 478 ASP cc_start: 0.8042 (m-30) cc_final: 0.7262 (m-30) REVERT: B 486 CYS cc_start: 0.8954 (t) cc_final: 0.8703 (t) REVERT: B 496 LEU cc_start: 0.8953 (mm) cc_final: 0.8617 (mm) REVERT: B 507 LEU cc_start: 0.8669 (tp) cc_final: 0.8438 (tt) REVERT: B 512 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8250 (mtm180) REVERT: B 528 ASP cc_start: 0.8185 (p0) cc_final: 0.7664 (p0) REVERT: B 546 LYS cc_start: 0.7989 (tppt) cc_final: 0.7465 (tppp) REVERT: B 556 TYR cc_start: 0.8730 (p90) cc_final: 0.8478 (p90) REVERT: B 576 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: B 580 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8340 (mmtm) REVERT: B 668 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7942 (tp) REVERT: B 669 ASP cc_start: 0.7385 (t0) cc_final: 0.7017 (t0) REVERT: B 677 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7629 (ttm-80) REVERT: B 681 LYS cc_start: 0.8944 (tptt) cc_final: 0.8553 (tppt) REVERT: B 691 TYR cc_start: 0.8186 (m-10) cc_final: 0.7834 (m-10) REVERT: B 698 ASP cc_start: 0.8034 (t0) cc_final: 0.7547 (t0) REVERT: B 701 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 714 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7580 (mtt90) REVERT: B 724 ASP cc_start: 0.8040 (t0) cc_final: 0.7446 (t70) REVERT: B 732 GLN cc_start: 0.8312 (tt0) cc_final: 0.7604 (tm-30) outliers start: 46 outliers final: 35 residues processed: 387 average time/residue: 0.2766 time to fit residues: 143.7324 Evaluate side-chains 389 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 261 PHE Chi-restraints excluded: chain A residue 385 PHE 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 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 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 433 VAL Chi-restraints excluded: chain B residue 512 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 98 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** B 375 HIS ** 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 = 0.111723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093822 restraints weight = 23234.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097167 restraints weight = 11986.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099307 restraints weight = 7358.411| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4749 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= 0.176 Angle : 0.817 20.509 14136 Z= 0.404 Chirality : 0.046 0.251 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.236 50.993 1427 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.74 % Allowed : 23.53 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1322 helix: 0.96 (0.18), residues: 832 sheet: -1.95 (0.76), residues: 48 loop : -1.82 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 83 HIS 0.017 0.002 HIS A 728 PHE 0.027 0.002 PHE B 394 TYR 0.034 0.002 TYR B 105 ARG 0.007 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 575) hydrogen bonds : angle 3.94585 ( 1683) covalent geometry : bond 0.00385 (10400) covalent geometry : angle 0.81696 (14136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4415.90 seconds wall clock time: 78 minutes 47.71 seconds (4727.71 seconds total)