Starting phenix.real_space_refine on Wed Sep 25 11:11:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_32576.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_32576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_32576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_32576.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl7_32576/09_2024/7wl7_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-5461/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: 6.32, per 1000 atoms: 0.62 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: 2.44 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: 0.98 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: 2.84 Time building geometry restraints manager: 2.84 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: 0.00 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: 2.430 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: 0.080 Process input model: 24.250 Find NCS groups from input model: 0.250 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- 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= 0.115 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 *********************** 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 fitting. rotamer outliers: 38 poor density : 394 time to evaluate : 1.099 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: 0.2778 time to fit residues: 151.6959 Evaluate side-chains 360 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 345 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 705 GLN 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 730 GLN B 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10400 Z= 0.226 Angle : 0.662 11.105 14136 Z= 0.343 Chirality : 0.043 0.167 1718 Planarity : 0.005 0.036 1758 Dihedral : 6.242 82.899 1445 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.63 % Allowed : 12.21 % Favored : 83.16 % 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: -1.63 (0.22), residues: 1322 helix: -0.12 (0.17), residues: 834 sheet: -3.02 (0.67), residues: 48 loop : -2.67 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.009 0.002 HIS A 656 PHE 0.023 0.002 PHE A 484 TYR 0.020 0.002 TYR A 377 ARG 0.005 0.001 ARG A 38 *********************** 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 415 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 363 time to evaluate : 1.023 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 46 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7067 (tm) REVERT: A 72 LEU cc_start: 0.9090 (mp) cc_final: 0.8800 (pp) REVERT: A 94 THR cc_start: 0.8333 (p) cc_final: 0.8109 (p) REVERT: A 121 PHE cc_start: 0.8100 (t80) cc_final: 0.7824 (t80) REVERT: A 122 PHE cc_start: 0.8152 (m-80) cc_final: 0.7688 (m-10) REVERT: A 145 SER cc_start: 0.8466 (m) cc_final: 0.8094 (p) REVERT: A 160 HIS cc_start: 0.6898 (t-90) cc_final: 0.6393 (t-90) REVERT: A 161 PHE cc_start: 0.7415 (m-80) cc_final: 0.6342 (m-80) REVERT: A 182 ASP cc_start: 0.8068 (m-30) cc_final: 0.7769 (m-30) REVERT: A 235 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7628 (mm-40) REVERT: A 238 ILE cc_start: 0.8502 (mt) cc_final: 0.8250 (tp) REVERT: A 242 VAL cc_start: 0.8935 (m) cc_final: 0.8667 (p) REVERT: A 262 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7517 (mm-40) REVERT: A 293 LYS cc_start: 0.8773 (tppt) cc_final: 0.8516 (tppt) REVERT: A 361 TYR cc_start: 0.8700 (t80) cc_final: 0.8440 (t80) REVERT: A 384 GLU cc_start: 0.7789 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 394 PHE cc_start: 0.8232 (t80) cc_final: 0.6887 (t80) REVERT: A 398 PHE cc_start: 0.6514 (m-80) cc_final: 0.5915 (m-80) REVERT: A 432 MET cc_start: 0.7715 (tpt) cc_final: 0.7410 (tpt) REVERT: A 435 ILE cc_start: 0.8923 (mt) cc_final: 0.8652 (tp) REVERT: A 459 LYS cc_start: 0.8867 (tppp) cc_final: 0.8605 (tppt) REVERT: A 470 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7378 (tpp80) REVERT: A 496 LEU cc_start: 0.8842 (mm) cc_final: 0.8593 (tp) REVERT: A 529 ILE cc_start: 0.8087 (tp) cc_final: 0.7852 (pt) REVERT: A 556 TYR cc_start: 0.8511 (p90) cc_final: 0.8299 (p90) REVERT: A 578 TYR cc_start: 0.7466 (t80) cc_final: 0.6896 (t80) REVERT: A 580 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8672 (mmtm) REVERT: A 582 LEU cc_start: 0.9000 (mm) cc_final: 0.8784 (mm) REVERT: A 678 MET cc_start: 0.6963 (tmm) cc_final: 0.5234 (tmm) REVERT: A 681 LYS cc_start: 0.9004 (tptt) cc_final: 0.8444 (mmmm) REVERT: A 685 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8205 (mtm180) REVERT: A 687 ASP cc_start: 0.8229 (t0) cc_final: 0.7804 (t0) REVERT: A 698 ASP cc_start: 0.7470 (t0) cc_final: 0.7254 (t0) REVERT: A 701 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 704 GLU cc_start: 0.7834 (tt0) cc_final: 0.7520 (tt0) REVERT: A 714 ARG cc_start: 0.7835 (ptp90) cc_final: 0.7542 (mtt90) REVERT: A 732 GLN cc_start: 0.8360 (tt0) cc_final: 0.7602 (tm-30) REVERT: B 36 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7661 (mmt-90) REVERT: B 46 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7088 (tm) REVERT: B 68 LEU cc_start: 0.8872 (tp) cc_final: 0.8555 (tp) REVERT: B 73 ASP cc_start: 0.7606 (t0) cc_final: 0.7325 (t0) REVERT: B 96 LEU cc_start: 0.9033 (mt) cc_final: 0.8732 (mm) REVERT: B 121 PHE cc_start: 0.7492 (t80) cc_final: 0.7232 (t80) REVERT: B 161 PHE cc_start: 0.7700 (m-80) cc_final: 0.6868 (m-80) REVERT: B 199 ILE cc_start: 0.9147 (mt) cc_final: 0.8922 (mt) REVERT: B 203 PHE cc_start: 0.8136 (m-80) cc_final: 0.7276 (m-80) REVERT: B 211 ILE cc_start: 0.8518 (tt) cc_final: 0.7758 (pt) REVERT: B 264 ILE cc_start: 0.8547 (mm) cc_final: 0.8343 (mm) REVERT: B 276 LEU cc_start: 0.8567 (tp) cc_final: 0.8300 (tt) REVERT: B 287 GLU cc_start: 0.8335 (tp30) cc_final: 0.7516 (tp30) REVERT: B 288 LEU cc_start: 0.8897 (tp) cc_final: 0.8632 (tp) REVERT: B 293 LYS cc_start: 0.8100 (tppt) cc_final: 0.7644 (tppt) REVERT: B 304 VAL cc_start: 0.8594 (t) cc_final: 0.8338 (p) REVERT: B 355 SER cc_start: 0.9087 (m) cc_final: 0.8780 (p) REVERT: B 383 GLN cc_start: 0.8182 (tp40) cc_final: 0.7714 (tp40) REVERT: B 384 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 421 GLN cc_start: 0.8053 (mm110) cc_final: 0.7809 (mm110) REVERT: B 426 ILE cc_start: 0.8770 (mt) cc_final: 0.8444 (tp) REVERT: B 432 MET cc_start: 0.7830 (tpt) cc_final: 0.7418 (tpt) REVERT: B 435 ILE cc_start: 0.8801 (mt) cc_final: 0.8518 (tp) REVERT: B 447 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8365 (mtpp) REVERT: B 470 ARG cc_start: 0.7774 (tpp80) cc_final: 0.7305 (tpp80) REVERT: B 473 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8385 (mppt) REVERT: B 475 ASN cc_start: 0.7104 (t0) cc_final: 0.6880 (t0) REVERT: B 484 PHE cc_start: 0.8413 (t80) cc_final: 0.8052 (t80) REVERT: B 486 CYS cc_start: 0.8634 (t) cc_final: 0.8397 (t) REVERT: B 580 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8429 (mmtm) REVERT: B 677 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7618 (ttm-80) REVERT: B 678 MET cc_start: 0.7252 (tpp) cc_final: 0.6803 (tpp) REVERT: B 681 LYS cc_start: 0.9032 (tptt) cc_final: 0.8535 (mmmm) REVERT: B 698 ASP cc_start: 0.7698 (t0) cc_final: 0.7308 (t0) REVERT: B 701 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 714 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7549 (mtt90) REVERT: B 727 LEU cc_start: 0.8702 (mt) cc_final: 0.8184 (mt) REVERT: B 732 GLN cc_start: 0.8040 (tt0) cc_final: 0.7331 (tm-30) outliers start: 52 outliers final: 28 residues processed: 388 average time/residue: 0.2373 time to fit residues: 124.0536 Evaluate side-chains 379 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 350 LEU Chi-restraints excluded: chain B residue 429 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 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 0.0370 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10400 Z= 0.194 Angle : 0.635 11.041 14136 Z= 0.325 Chirality : 0.042 0.160 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.236 55.004 1434 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.92 % Allowed : 14.44 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1322 helix: 0.52 (0.18), residues: 828 sheet: -2.26 (0.87), residues: 36 loop : -2.23 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.011 0.002 HIS B 728 PHE 0.022 0.001 PHE A 354 TYR 0.016 0.001 TYR A 377 ARG 0.007 0.001 ARG B 39 *********************** 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 379 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.143 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 46 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7084 (tm) REVERT: A 83 TRP cc_start: 0.6617 (m-10) cc_final: 0.6317 (m-10) REVERT: A 94 THR cc_start: 0.8295 (p) cc_final: 0.7943 (p) REVERT: A 96 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 97 VAL cc_start: 0.8997 (t) cc_final: 0.8626 (p) REVERT: A 121 PHE cc_start: 0.8026 (t80) cc_final: 0.7675 (t80) REVERT: A 122 PHE cc_start: 0.8115 (m-80) cc_final: 0.7712 (m-10) REVERT: A 145 SER cc_start: 0.8491 (m) cc_final: 0.8118 (p) REVERT: A 160 HIS cc_start: 0.6785 (t-90) cc_final: 0.6279 (t-90) REVERT: A 161 PHE cc_start: 0.7454 (m-80) cc_final: 0.6560 (m-80) REVERT: A 182 ASP cc_start: 0.8064 (m-30) cc_final: 0.7791 (m-30) REVERT: A 188 LEU cc_start: 0.9026 (tp) cc_final: 0.8782 (tt) REVERT: A 235 GLN cc_start: 0.7797 (mm110) cc_final: 0.7581 (mm-40) REVERT: A 238 ILE cc_start: 0.8549 (mt) cc_final: 0.8259 (tp) REVERT: A 242 VAL cc_start: 0.8917 (m) cc_final: 0.8615 (p) REVERT: A 258 ILE cc_start: 0.8726 (mm) cc_final: 0.8387 (tp) REVERT: A 293 LYS cc_start: 0.8828 (tppt) cc_final: 0.8499 (tppt) REVERT: A 384 GLU cc_start: 0.7795 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 394 PHE cc_start: 0.8296 (t80) cc_final: 0.7636 (t80) REVERT: A 426 ILE cc_start: 0.8848 (mt) cc_final: 0.8570 (tp) REVERT: A 432 MET cc_start: 0.7642 (tpt) cc_final: 0.7338 (tpt) REVERT: A 435 ILE cc_start: 0.8899 (mt) cc_final: 0.8659 (tp) REVERT: A 470 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7475 (tpp80) REVERT: A 496 LEU cc_start: 0.8869 (mm) cc_final: 0.8540 (mm) REVERT: A 529 ILE cc_start: 0.8102 (tp) cc_final: 0.7895 (pt) REVERT: A 537 LYS cc_start: 0.8229 (mtpp) cc_final: 0.6996 (mtmt) REVERT: A 543 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 556 TYR cc_start: 0.8519 (p90) cc_final: 0.8257 (p90) REVERT: A 578 TYR cc_start: 0.7425 (t80) cc_final: 0.6694 (t80) REVERT: A 580 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8662 (mmtm) REVERT: A 582 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 678 MET cc_start: 0.7106 (tmm) cc_final: 0.6435 (tmm) REVERT: A 681 LYS cc_start: 0.8994 (tptt) cc_final: 0.8475 (mmmm) REVERT: A 682 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6926 (mt-10) REVERT: A 685 ARG cc_start: 0.8414 (mtm180) cc_final: 0.8161 (mtm110) REVERT: A 687 ASP cc_start: 0.8201 (t0) cc_final: 0.7780 (t0) REVERT: A 694 LEU cc_start: 0.8827 (mm) cc_final: 0.8534 (mt) REVERT: A 701 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 704 GLU cc_start: 0.7848 (tt0) cc_final: 0.7562 (tt0) REVERT: A 714 ARG cc_start: 0.7778 (ptp90) cc_final: 0.7545 (mtt90) REVERT: A 732 GLN cc_start: 0.8278 (tt0) cc_final: 0.7536 (tm-30) REVERT: B 36 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7480 (mmt-90) REVERT: B 46 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7121 (tm) REVERT: B 68 LEU cc_start: 0.8883 (tp) cc_final: 0.8603 (tp) REVERT: B 73 ASP cc_start: 0.7647 (t0) cc_final: 0.7386 (t0) REVERT: B 130 PHE cc_start: 0.7904 (m-80) cc_final: 0.7633 (m-10) REVERT: B 161 PHE cc_start: 0.7622 (m-80) cc_final: 0.7057 (m-80) REVERT: B 182 ASP cc_start: 0.7602 (p0) cc_final: 0.7318 (p0) REVERT: B 199 ILE cc_start: 0.9138 (mt) cc_final: 0.8892 (mt) REVERT: B 203 PHE cc_start: 0.8082 (m-80) cc_final: 0.7381 (m-80) REVERT: B 211 ILE cc_start: 0.8435 (tt) cc_final: 0.7822 (pt) REVERT: B 264 ILE cc_start: 0.8666 (mm) cc_final: 0.8426 (mm) REVERT: B 276 LEU cc_start: 0.8534 (tp) cc_final: 0.8227 (tt) REVERT: B 288 LEU cc_start: 0.8845 (tp) cc_final: 0.8618 (tp) REVERT: B 291 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7319 (ttp-110) REVERT: B 292 PHE cc_start: 0.7067 (t80) cc_final: 0.6859 (t80) REVERT: B 293 LYS cc_start: 0.8080 (tppt) cc_final: 0.7723 (tppt) REVERT: B 355 SER cc_start: 0.9058 (m) cc_final: 0.8799 (p) REVERT: B 369 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8437 (mtmt) REVERT: B 383 GLN cc_start: 0.8081 (tp40) cc_final: 0.7660 (tp40) REVERT: B 384 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 413 GLN cc_start: 0.7829 (pt0) cc_final: 0.7299 (pp30) REVERT: B 426 ILE cc_start: 0.8777 (mt) cc_final: 0.8462 (tp) REVERT: B 432 MET cc_start: 0.7842 (tpt) cc_final: 0.7528 (tpt) REVERT: B 435 ILE cc_start: 0.8871 (mt) cc_final: 0.8668 (tp) REVERT: B 470 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7306 (tpp80) REVERT: B 475 ASN cc_start: 0.7011 (t0) cc_final: 0.6706 (t0) REVERT: B 486 CYS cc_start: 0.8560 (t) cc_final: 0.8321 (t) REVERT: B 495 ASP cc_start: 0.8039 (p0) cc_final: 0.7783 (p0) REVERT: B 496 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8389 (mm) REVERT: B 499 LEU cc_start: 0.8866 (tp) cc_final: 0.8562 (tp) REVERT: B 507 LEU cc_start: 0.8499 (tp) cc_final: 0.8206 (tt) REVERT: B 578 TYR cc_start: 0.7440 (t80) cc_final: 0.7234 (t80) REVERT: B 580 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8376 (mmtm) REVERT: B 677 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7648 (ttm-80) REVERT: B 678 MET cc_start: 0.7327 (tpp) cc_final: 0.6929 (tpp) REVERT: B 681 LYS cc_start: 0.9000 (tptt) cc_final: 0.8506 (mmmm) REVERT: B 698 ASP cc_start: 0.7679 (t0) cc_final: 0.7438 (t70) REVERT: B 701 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 714 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7538 (mtt90) REVERT: B 727 LEU cc_start: 0.8673 (mt) cc_final: 0.8372 (mt) REVERT: B 732 GLN cc_start: 0.7986 (tt0) cc_final: 0.7309 (tm-30) outliers start: 44 outliers final: 27 residues processed: 359 average time/residue: 0.2538 time to fit residues: 122.2062 Evaluate side-chains 354 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 322 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 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 212 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 208 ILE 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 405 THR 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 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 375 HIS A 382 ASN A 457 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10400 Z= 0.228 Angle : 0.637 9.959 14136 Z= 0.329 Chirality : 0.043 0.210 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.276 56.596 1434 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.37 % Allowed : 15.86 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1322 helix: 0.84 (0.18), residues: 836 sheet: -2.02 (0.88), residues: 36 loop : -2.22 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 83 HIS 0.012 0.001 HIS B 728 PHE 0.021 0.001 PHE A 354 TYR 0.017 0.002 TYR A 27 ARG 0.010 0.001 ARG B 39 *********************** 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 378 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 329 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.8364 (m-10) cc_final: 0.8131 (m-10) REVERT: A 46 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7113 (tm) REVERT: A 66 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8093 (mmtt) REVERT: A 83 TRP cc_start: 0.6664 (m-10) cc_final: 0.6304 (m-10) REVERT: A 96 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 97 VAL cc_start: 0.9076 (t) cc_final: 0.8772 (p) REVERT: A 121 PHE cc_start: 0.8111 (t80) cc_final: 0.7762 (t80) REVERT: A 122 PHE cc_start: 0.8140 (m-80) cc_final: 0.7666 (m-10) REVERT: A 145 SER cc_start: 0.8517 (m) cc_final: 0.8139 (p) REVERT: A 160 HIS cc_start: 0.6905 (t-90) cc_final: 0.6617 (t-90) REVERT: A 161 PHE cc_start: 0.7547 (m-80) cc_final: 0.6918 (m-80) REVERT: A 182 ASP cc_start: 0.8120 (m-30) cc_final: 0.7837 (m-30) REVERT: A 188 LEU cc_start: 0.9022 (tp) cc_final: 0.8537 (tt) REVERT: A 200 GLN cc_start: 0.8131 (tt0) cc_final: 0.7830 (tt0) REVERT: A 235 GLN cc_start: 0.7825 (mm110) cc_final: 0.7561 (mm-40) REVERT: A 238 ILE cc_start: 0.8624 (mt) cc_final: 0.8389 (mt) REVERT: A 242 VAL cc_start: 0.8912 (m) cc_final: 0.8590 (p) REVERT: A 293 LYS cc_start: 0.8840 (tppt) cc_final: 0.8485 (tppt) REVERT: A 355 SER cc_start: 0.8885 (m) cc_final: 0.8660 (p) REVERT: A 361 TYR cc_start: 0.8685 (t80) cc_final: 0.8475 (t80) REVERT: A 371 TYR cc_start: 0.7125 (m-80) cc_final: 0.6905 (m-80) REVERT: A 384 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 394 PHE cc_start: 0.8337 (t80) cc_final: 0.7657 (t80) REVERT: A 432 MET cc_start: 0.7703 (tpt) cc_final: 0.7398 (tpt) REVERT: A 435 ILE cc_start: 0.8959 (mt) cc_final: 0.8706 (tp) REVERT: A 470 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7577 (tpp80) REVERT: A 496 LEU cc_start: 0.8908 (mm) cc_final: 0.8597 (tp) REVERT: A 529 ILE cc_start: 0.8117 (tp) cc_final: 0.7869 (pt) REVERT: A 530 TYR cc_start: 0.8261 (m-80) cc_final: 0.8027 (m-10) REVERT: A 543 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 556 TYR cc_start: 0.8597 (p90) cc_final: 0.8312 (p90) REVERT: A 578 TYR cc_start: 0.7406 (t80) cc_final: 0.6869 (t80) REVERT: A 580 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8686 (mmtm) REVERT: A 582 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 678 MET cc_start: 0.7184 (tmm) cc_final: 0.6895 (tmm) REVERT: A 681 LYS cc_start: 0.9037 (tptt) cc_final: 0.8533 (mmmm) REVERT: A 685 ARG cc_start: 0.8386 (mtm180) cc_final: 0.8158 (mtm180) REVERT: A 687 ASP cc_start: 0.8207 (t0) cc_final: 0.7893 (t0) REVERT: A 694 LEU cc_start: 0.8868 (mm) cc_final: 0.8557 (mt) REVERT: A 701 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 704 GLU cc_start: 0.7877 (tt0) cc_final: 0.7554 (tt0) REVERT: A 714 ARG cc_start: 0.7795 (ptp90) cc_final: 0.7523 (mtt90) REVERT: A 732 GLN cc_start: 0.8274 (tt0) cc_final: 0.7630 (tm-30) REVERT: B 36 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7421 (mmt-90) REVERT: B 46 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7138 (tm) REVERT: B 68 LEU cc_start: 0.8894 (tp) cc_final: 0.8608 (tp) REVERT: B 73 ASP cc_start: 0.7697 (t0) cc_final: 0.7432 (t0) REVERT: B 96 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 161 PHE cc_start: 0.7891 (m-80) cc_final: 0.7392 (m-10) REVERT: B 203 PHE cc_start: 0.8070 (m-80) cc_final: 0.7710 (m-80) REVERT: B 211 ILE cc_start: 0.8479 (tt) cc_final: 0.8045 (pt) REVERT: B 213 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7279 (mtm-85) REVERT: B 264 ILE cc_start: 0.8807 (mm) cc_final: 0.8565 (mm) REVERT: B 276 LEU cc_start: 0.8574 (tp) cc_final: 0.8278 (tt) REVERT: B 286 LYS cc_start: 0.8830 (tppt) cc_final: 0.8623 (ptmm) REVERT: B 288 LEU cc_start: 0.8900 (tp) cc_final: 0.8666 (tp) REVERT: B 291 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7339 (ttp-110) REVERT: B 292 PHE cc_start: 0.7134 (t80) cc_final: 0.6818 (t80) REVERT: B 293 LYS cc_start: 0.8146 (tppt) cc_final: 0.7630 (tppt) REVERT: B 355 SER cc_start: 0.9015 (m) cc_final: 0.8769 (p) REVERT: B 369 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8380 (pttt) REVERT: B 371 TYR cc_start: 0.7237 (m-80) cc_final: 0.6946 (m-80) REVERT: B 383 GLN cc_start: 0.8111 (tp40) cc_final: 0.7748 (tp40) REVERT: B 384 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 413 GLN cc_start: 0.7871 (pt0) cc_final: 0.7439 (pp30) REVERT: B 421 GLN cc_start: 0.8051 (mm110) cc_final: 0.7818 (mm110) REVERT: B 426 ILE cc_start: 0.8827 (mt) cc_final: 0.8506 (tp) REVERT: B 432 MET cc_start: 0.7912 (tpt) cc_final: 0.7424 (tpt) REVERT: B 435 ILE cc_start: 0.8962 (mt) cc_final: 0.8725 (tp) REVERT: B 447 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8425 (mtpp) REVERT: B 470 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7442 (tpp80) REVERT: B 486 CYS cc_start: 0.8596 (t) cc_final: 0.8357 (t) REVERT: B 496 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 507 LEU cc_start: 0.8552 (tp) cc_final: 0.8275 (tt) REVERT: B 546 LYS cc_start: 0.8050 (tppt) cc_final: 0.7849 (tppt) REVERT: B 580 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8393 (mmtm) REVERT: B 587 ARG cc_start: 0.6838 (tpt170) cc_final: 0.6634 (tpt170) REVERT: B 677 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7667 (ttm-80) REVERT: B 678 MET cc_start: 0.7393 (tpp) cc_final: 0.6951 (tpp) REVERT: B 681 LYS cc_start: 0.9041 (tptt) cc_final: 0.8511 (mmmm) REVERT: B 685 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8307 (mtm-85) REVERT: B 698 ASP cc_start: 0.7752 (t0) cc_final: 0.7329 (t70) REVERT: B 701 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 714 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7541 (mtt90) REVERT: B 728 HIS cc_start: 0.8717 (t-170) cc_final: 0.8184 (t-170) REVERT: B 732 GLN cc_start: 0.7986 (tt0) cc_final: 0.7600 (tm-30) outliers start: 49 outliers final: 31 residues processed: 355 average time/residue: 0.2543 time to fit residues: 120.9607 Evaluate side-chains 362 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 325 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 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 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 405 THR 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 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 0.053 10400 Z= 0.216 Angle : 0.671 13.081 14136 Z= 0.341 Chirality : 0.043 0.176 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.390 59.603 1434 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.72 % Allowed : 17.83 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1322 helix: 0.89 (0.18), residues: 840 sheet: -1.90 (0.88), residues: 36 loop : -2.06 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 83 HIS 0.016 0.003 HIS B 375 PHE 0.024 0.001 PHE A 484 TYR 0.016 0.001 TYR B 377 ARG 0.011 0.000 ARG B 39 *********************** 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 384 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7933 (mmtt) REVERT: A 96 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 97 VAL cc_start: 0.9077 (t) cc_final: 0.8775 (p) REVERT: A 121 PHE cc_start: 0.8093 (t80) cc_final: 0.7745 (t80) REVERT: A 122 PHE cc_start: 0.8138 (m-80) cc_final: 0.7712 (m-80) REVERT: A 145 SER cc_start: 0.8546 (m) cc_final: 0.8181 (p) REVERT: A 160 HIS cc_start: 0.6900 (t-90) cc_final: 0.6604 (t-90) REVERT: A 161 PHE cc_start: 0.7589 (m-80) cc_final: 0.6978 (m-80) REVERT: A 182 ASP cc_start: 0.8126 (m-30) cc_final: 0.7852 (m-30) REVERT: A 235 GLN cc_start: 0.7769 (mm110) cc_final: 0.7557 (mm-40) REVERT: A 238 ILE cc_start: 0.8628 (mt) cc_final: 0.8394 (mt) REVERT: A 242 VAL cc_start: 0.8909 (m) cc_final: 0.8588 (p) REVERT: A 258 ILE cc_start: 0.8818 (tp) cc_final: 0.8501 (pt) REVERT: A 293 LYS cc_start: 0.8843 (tppt) cc_final: 0.8475 (tppt) REVERT: A 361 TYR cc_start: 0.8696 (t80) cc_final: 0.8486 (t80) REVERT: A 371 TYR cc_start: 0.7076 (m-80) cc_final: 0.6838 (m-80) REVERT: A 384 GLU cc_start: 0.7916 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 394 PHE cc_start: 0.8348 (t80) cc_final: 0.7485 (t80) REVERT: A 432 MET cc_start: 0.7697 (tpt) cc_final: 0.7329 (tpt) REVERT: A 435 ILE cc_start: 0.8962 (mt) cc_final: 0.8713 (tp) REVERT: A 470 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7577 (tpp80) REVERT: A 496 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 519 ASN cc_start: 0.8093 (m110) cc_final: 0.7891 (m110) REVERT: A 529 ILE cc_start: 0.8166 (tp) cc_final: 0.7918 (pt) REVERT: A 537 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7295 (ptpp) REVERT: A 543 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 556 TYR cc_start: 0.8591 (p90) cc_final: 0.8337 (p90) REVERT: A 578 TYR cc_start: 0.7414 (t80) cc_final: 0.6666 (t80) REVERT: A 580 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8486 (mmmt) REVERT: A 582 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8783 (mm) REVERT: A 677 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7556 (ttm-80) REVERT: A 681 LYS cc_start: 0.9049 (tptt) cc_final: 0.8520 (mmmm) REVERT: A 682 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 685 ARG cc_start: 0.8372 (mtm180) cc_final: 0.8172 (mtm110) REVERT: A 687 ASP cc_start: 0.8204 (t0) cc_final: 0.7871 (t0) REVERT: A 694 LEU cc_start: 0.8853 (mm) cc_final: 0.8511 (mt) REVERT: A 701 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 704 GLU cc_start: 0.7883 (tt0) cc_final: 0.7593 (tt0) REVERT: A 714 ARG cc_start: 0.7794 (ptp90) cc_final: 0.7540 (mtt90) REVERT: A 732 GLN cc_start: 0.8281 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 36 ARG cc_start: 0.7924 (tpp-160) cc_final: 0.7500 (mmt-90) REVERT: B 46 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7129 (tm) REVERT: B 68 LEU cc_start: 0.8899 (tp) cc_final: 0.8632 (tp) REVERT: B 73 ASP cc_start: 0.7705 (t0) cc_final: 0.7400 (t0) REVERT: B 96 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8809 (mm) REVERT: B 118 TYR cc_start: 0.7885 (m-10) cc_final: 0.7446 (m-80) REVERT: B 121 PHE cc_start: 0.7580 (t80) cc_final: 0.7352 (t80) REVERT: B 161 PHE cc_start: 0.7835 (m-80) cc_final: 0.7414 (m-10) REVERT: B 203 PHE cc_start: 0.8164 (m-80) cc_final: 0.7689 (m-80) REVERT: B 211 ILE cc_start: 0.8459 (tt) cc_final: 0.8031 (pt) REVERT: B 287 GLU cc_start: 0.8294 (tp30) cc_final: 0.7586 (tp30) REVERT: B 288 LEU cc_start: 0.8873 (tp) cc_final: 0.8630 (tp) REVERT: B 292 PHE cc_start: 0.7136 (t80) cc_final: 0.6803 (t80) REVERT: B 293 LYS cc_start: 0.8188 (tppt) cc_final: 0.7684 (tppt) REVERT: B 355 SER cc_start: 0.9027 (m) cc_final: 0.8781 (p) REVERT: B 361 TYR cc_start: 0.8712 (t80) cc_final: 0.8448 (t80) REVERT: B 369 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8368 (pttt) REVERT: B 371 TYR cc_start: 0.7331 (m-80) cc_final: 0.6841 (m-80) REVERT: B 377 TYR cc_start: 0.6948 (p90) cc_final: 0.5765 (p90) REVERT: B 383 GLN cc_start: 0.8131 (tp40) cc_final: 0.7807 (tp40) REVERT: B 384 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 413 GLN cc_start: 0.7886 (pt0) cc_final: 0.7398 (tm-30) REVERT: B 422 VAL cc_start: 0.8576 (t) cc_final: 0.8321 (m) REVERT: B 426 ILE cc_start: 0.8811 (mt) cc_final: 0.8514 (tp) REVERT: B 432 MET cc_start: 0.7855 (tpt) cc_final: 0.7426 (tpt) REVERT: B 435 ILE cc_start: 0.8978 (mt) cc_final: 0.8753 (tp) REVERT: B 447 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8352 (mtpp) REVERT: B 470 ARG cc_start: 0.7915 (tpp80) cc_final: 0.7434 (tpp80) REVERT: B 486 CYS cc_start: 0.8517 (t) cc_final: 0.8267 (t) REVERT: B 495 ASP cc_start: 0.8071 (p0) cc_final: 0.7835 (p0) REVERT: B 496 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8430 (mm) REVERT: B 507 LEU cc_start: 0.8514 (tp) cc_final: 0.8236 (tt) REVERT: B 546 LYS cc_start: 0.8058 (tppt) cc_final: 0.7816 (tppt) REVERT: B 580 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8360 (mmtm) REVERT: B 677 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7737 (tpp80) REVERT: B 678 MET cc_start: 0.7388 (tpp) cc_final: 0.6921 (tpp) REVERT: B 681 LYS cc_start: 0.9036 (tptt) cc_final: 0.8508 (mmmm) REVERT: B 685 ARG cc_start: 0.8545 (mtm180) cc_final: 0.8334 (mtm-85) REVERT: B 698 ASP cc_start: 0.7757 (t0) cc_final: 0.7322 (t70) REVERT: B 701 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 714 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7541 (mtt90) REVERT: B 732 GLN cc_start: 0.8307 (tt0) cc_final: 0.7458 (tm-30) outliers start: 53 outliers final: 37 residues processed: 356 average time/residue: 0.2416 time to fit residues: 115.6417 Evaluate side-chains 374 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 331 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 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 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 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 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 252 SER Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 405 THR 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 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 446 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.050 10400 Z= 0.212 Angle : 0.675 12.272 14136 Z= 0.341 Chirality : 0.043 0.222 1718 Planarity : 0.004 0.038 1758 Dihedral : 5.328 57.567 1432 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.46 % Allowed : 19.16 % Favored : 76.38 % 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: -0.12 (0.24), residues: 1322 helix: 0.99 (0.18), residues: 830 sheet: -1.73 (0.87), residues: 36 loop : -1.97 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 83 HIS 0.012 0.002 HIS A 375 PHE 0.022 0.001 PHE A 354 TYR 0.021 0.002 TYR B 105 ARG 0.011 0.001 ARG B 39 *********************** 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 387 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 337 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7406 (ttm110) cc_final: 0.7099 (mtp85) REVERT: A 66 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7975 (mmtt) REVERT: A 96 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 97 VAL cc_start: 0.9069 (t) cc_final: 0.8764 (p) REVERT: A 121 PHE cc_start: 0.8086 (t80) cc_final: 0.7737 (t80) REVERT: A 122 PHE cc_start: 0.8135 (m-80) cc_final: 0.7683 (m-80) REVERT: A 145 SER cc_start: 0.8532 (m) cc_final: 0.8183 (p) REVERT: A 160 HIS cc_start: 0.6915 (t-90) cc_final: 0.6644 (t-90) REVERT: A 161 PHE cc_start: 0.7599 (m-80) cc_final: 0.7056 (m-80) REVERT: A 182 ASP cc_start: 0.8094 (m-30) cc_final: 0.7641 (m-30) REVERT: A 193 THR cc_start: 0.8607 (m) cc_final: 0.8329 (p) REVERT: A 235 GLN cc_start: 0.7743 (mm110) cc_final: 0.7516 (mm-40) REVERT: A 238 ILE cc_start: 0.8639 (mt) cc_final: 0.8396 (mt) REVERT: A 258 ILE cc_start: 0.8817 (tp) cc_final: 0.8499 (pt) REVERT: A 293 LYS cc_start: 0.8852 (tppt) cc_final: 0.8469 (tppt) REVERT: A 384 GLU cc_start: 0.7910 (mm-30) cc_final: 0.6888 (mm-30) REVERT: A 394 PHE cc_start: 0.8364 (t80) cc_final: 0.7461 (t80) REVERT: A 432 MET cc_start: 0.7689 (tpt) cc_final: 0.7319 (tpt) REVERT: A 435 ILE cc_start: 0.8967 (mt) cc_final: 0.8719 (tp) REVERT: A 459 LYS cc_start: 0.8974 (tppp) cc_final: 0.8576 (tppt) REVERT: A 464 GLN cc_start: 0.8443 (tt0) cc_final: 0.7746 (tp-100) REVERT: A 470 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7588 (tpp80) REVERT: A 496 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 514 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 519 ASN cc_start: 0.8106 (m110) cc_final: 0.7786 (m-40) REVERT: A 529 ILE cc_start: 0.8156 (tp) cc_final: 0.7919 (pt) REVERT: A 530 TYR cc_start: 0.8117 (m-10) cc_final: 0.7909 (m-10) REVERT: A 537 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7337 (ptpp) REVERT: A 543 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 556 TYR cc_start: 0.8608 (p90) cc_final: 0.8353 (p90) REVERT: A 578 TYR cc_start: 0.7434 (t80) cc_final: 0.6678 (t80) REVERT: A 579 ASN cc_start: 0.8238 (p0) cc_final: 0.7893 (p0) REVERT: A 580 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8587 (mmmt) REVERT: A 582 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8800 (mm) REVERT: A 677 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7560 (ttm-80) REVERT: A 681 LYS cc_start: 0.9054 (tptt) cc_final: 0.8519 (mmmm) REVERT: A 687 ASP cc_start: 0.8213 (t0) cc_final: 0.7883 (t0) REVERT: A 694 LEU cc_start: 0.8875 (mm) cc_final: 0.8536 (mt) REVERT: A 701 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 704 GLU cc_start: 0.7866 (tt0) cc_final: 0.7586 (tt0) REVERT: A 714 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7542 (mtt90) REVERT: A 732 GLN cc_start: 0.8280 (tt0) cc_final: 0.7655 (tm-30) REVERT: B 36 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.7503 (mmt-90) REVERT: B 46 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7134 (tm) REVERT: B 66 LYS cc_start: 0.8858 (tppt) cc_final: 0.8283 (tppt) REVERT: B 68 LEU cc_start: 0.8900 (tp) cc_final: 0.8622 (tp) REVERT: B 96 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8807 (mm) REVERT: B 101 GLN cc_start: 0.8450 (tt0) cc_final: 0.8112 (tt0) REVERT: B 105 TYR cc_start: 0.8422 (m-80) cc_final: 0.8195 (m-80) REVERT: B 118 TYR cc_start: 0.7881 (m-10) cc_final: 0.7443 (m-80) REVERT: B 161 PHE cc_start: 0.7849 (m-80) cc_final: 0.7560 (m-10) REVERT: B 203 PHE cc_start: 0.8120 (m-80) cc_final: 0.7666 (m-80) REVERT: B 211 ILE cc_start: 0.8450 (tt) cc_final: 0.8018 (pt) REVERT: B 286 LYS cc_start: 0.8722 (ptmm) cc_final: 0.8259 (ptmt) REVERT: B 287 GLU cc_start: 0.8352 (tp30) cc_final: 0.7560 (tp30) REVERT: B 288 LEU cc_start: 0.8890 (tp) cc_final: 0.8646 (tp) REVERT: B 292 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 293 LYS cc_start: 0.8182 (tppt) cc_final: 0.7714 (tppt) REVERT: B 355 SER cc_start: 0.8984 (m) cc_final: 0.8720 (p) REVERT: B 361 TYR cc_start: 0.8705 (t80) cc_final: 0.8422 (t80) REVERT: B 369 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8335 (pttt) REVERT: B 371 TYR cc_start: 0.7310 (m-80) cc_final: 0.6997 (m-80) REVERT: B 383 GLN cc_start: 0.8144 (tp40) cc_final: 0.7857 (tp40) REVERT: B 384 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 413 GLN cc_start: 0.7867 (pt0) cc_final: 0.7527 (tm-30) REVERT: B 422 VAL cc_start: 0.8538 (t) cc_final: 0.8279 (m) REVERT: B 426 ILE cc_start: 0.8821 (mt) cc_final: 0.8523 (tp) REVERT: B 432 MET cc_start: 0.7854 (tpt) cc_final: 0.7434 (tpt) REVERT: B 435 ILE cc_start: 0.8995 (mt) cc_final: 0.8754 (tp) REVERT: B 447 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8440 (mtpp) REVERT: B 470 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7439 (tpp80) REVERT: B 486 CYS cc_start: 0.8504 (t) cc_final: 0.8241 (t) REVERT: B 496 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8470 (mm) REVERT: B 507 LEU cc_start: 0.8522 (tp) cc_final: 0.8244 (tt) REVERT: B 580 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8357 (mmtm) REVERT: B 587 ARG cc_start: 0.6829 (tpt170) cc_final: 0.6625 (tpt170) REVERT: B 677 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7571 (ttm-80) REVERT: B 678 MET cc_start: 0.7358 (tpp) cc_final: 0.6931 (tpp) REVERT: B 681 LYS cc_start: 0.9037 (tptt) cc_final: 0.8514 (mmmm) REVERT: B 698 ASP cc_start: 0.7777 (t0) cc_final: 0.7350 (t70) REVERT: B 701 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 714 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7566 (mtt90) REVERT: B 732 GLN cc_start: 0.8288 (tt0) cc_final: 0.7480 (tm-30) outliers start: 50 outliers final: 35 residues processed: 359 average time/residue: 0.2553 time to fit residues: 122.9661 Evaluate side-chains 370 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 328 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU 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 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 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 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 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4388 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= 0.202 Angle : 0.686 11.922 14136 Z= 0.346 Chirality : 0.043 0.204 1718 Planarity : 0.004 0.037 1758 Dihedral : 5.321 53.401 1432 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.72 % Allowed : 19.70 % Favored : 75.58 % 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: 0.02 (0.24), residues: 1322 helix: 1.04 (0.18), residues: 820 sheet: -1.65 (0.87), residues: 36 loop : -1.72 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 83 HIS 0.019 0.003 HIS A 375 PHE 0.033 0.002 PHE B 121 TYR 0.031 0.002 TYR A 361 ARG 0.012 0.001 ARG B 39 *********************** 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 382 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7977 (mmtt) REVERT: A 83 TRP cc_start: 0.6554 (m-10) cc_final: 0.6352 (m-10) REVERT: A 96 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 97 VAL cc_start: 0.9039 (t) cc_final: 0.8742 (p) REVERT: A 121 PHE cc_start: 0.8058 (t80) cc_final: 0.7786 (t80) REVERT: A 122 PHE cc_start: 0.8118 (m-80) cc_final: 0.7573 (m-10) REVERT: A 145 SER cc_start: 0.8514 (m) cc_final: 0.8149 (p) REVERT: A 160 HIS cc_start: 0.6902 (t-90) cc_final: 0.6663 (t-90) REVERT: A 161 PHE cc_start: 0.7595 (m-80) cc_final: 0.7104 (m-80) REVERT: A 193 THR cc_start: 0.8569 (m) cc_final: 0.8295 (p) REVERT: A 200 GLN cc_start: 0.8060 (tt0) cc_final: 0.7750 (tt0) REVERT: A 235 GLN cc_start: 0.7696 (mm110) cc_final: 0.7492 (mm-40) REVERT: A 238 ILE cc_start: 0.8621 (mt) cc_final: 0.8384 (mt) REVERT: A 258 ILE cc_start: 0.8815 (tp) cc_final: 0.8539 (pt) REVERT: A 293 LYS cc_start: 0.8822 (tppt) cc_final: 0.8463 (tppt) REVERT: A 361 TYR cc_start: 0.8633 (t80) cc_final: 0.8329 (t80) REVERT: A 384 GLU cc_start: 0.7885 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 394 PHE cc_start: 0.8367 (t80) cc_final: 0.7670 (t80) REVERT: A 432 MET cc_start: 0.7661 (tpt) cc_final: 0.7361 (tpt) REVERT: A 435 ILE cc_start: 0.8959 (mt) cc_final: 0.8718 (tp) REVERT: A 459 LYS cc_start: 0.8979 (tppp) cc_final: 0.8597 (tppt) REVERT: A 464 GLN cc_start: 0.8426 (tt0) cc_final: 0.7356 (tp-100) REVERT: A 467 ASP cc_start: 0.7886 (p0) cc_final: 0.5717 (p0) REVERT: A 470 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7569 (tpp80) REVERT: A 496 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 519 ASN cc_start: 0.8109 (m110) cc_final: 0.7739 (m-40) REVERT: A 529 ILE cc_start: 0.8157 (tp) cc_final: 0.7925 (pt) REVERT: A 530 TYR cc_start: 0.8081 (m-10) cc_final: 0.7838 (m-10) REVERT: A 537 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7363 (ptpp) REVERT: A 543 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 556 TYR cc_start: 0.8572 (p90) cc_final: 0.8279 (p90) REVERT: A 578 TYR cc_start: 0.7518 (t80) cc_final: 0.7148 (t80) REVERT: A 579 ASN cc_start: 0.8187 (p0) cc_final: 0.7584 (p0) REVERT: A 580 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8590 (mmtm) REVERT: A 582 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8775 (mm) REVERT: A 677 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7550 (ttm-80) REVERT: A 681 LYS cc_start: 0.8992 (tptt) cc_final: 0.8517 (mmmm) REVERT: A 682 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 687 ASP cc_start: 0.8218 (t0) cc_final: 0.7752 (t0) REVERT: A 694 LEU cc_start: 0.8848 (mm) cc_final: 0.8500 (mt) REVERT: A 698 ASP cc_start: 0.7559 (t0) cc_final: 0.7334 (t0) REVERT: A 701 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 704 GLU cc_start: 0.7844 (tt0) cc_final: 0.7561 (tt0) REVERT: A 714 ARG cc_start: 0.7786 (ptp90) cc_final: 0.7539 (mtt90) REVERT: A 732 GLN cc_start: 0.8275 (tt0) cc_final: 0.7716 (tm-30) REVERT: B 36 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7539 (mmt-90) REVERT: B 46 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7129 (tm) REVERT: B 66 LYS cc_start: 0.8869 (tppt) cc_final: 0.8574 (tppt) REVERT: B 68 LEU cc_start: 0.8884 (tp) cc_final: 0.8586 (tp) REVERT: B 118 TYR cc_start: 0.7876 (m-10) cc_final: 0.7436 (m-80) REVERT: B 182 ASP cc_start: 0.7589 (p0) cc_final: 0.7281 (p0) REVERT: B 193 THR cc_start: 0.8751 (m) cc_final: 0.8466 (p) REVERT: B 203 PHE cc_start: 0.8072 (m-80) cc_final: 0.7609 (m-80) REVERT: B 211 ILE cc_start: 0.8392 (tt) cc_final: 0.7927 (pt) REVERT: B 240 LEU cc_start: 0.9187 (mt) cc_final: 0.8802 (tt) REVERT: B 287 GLU cc_start: 0.8336 (tp30) cc_final: 0.7525 (tp30) REVERT: B 288 LEU cc_start: 0.8837 (tp) cc_final: 0.8555 (tp) REVERT: B 292 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6740 (t80) REVERT: B 293 LYS cc_start: 0.8194 (tppt) cc_final: 0.7726 (tppt) REVERT: B 355 SER cc_start: 0.8948 (m) cc_final: 0.8681 (p) REVERT: B 361 TYR cc_start: 0.8703 (t80) cc_final: 0.8408 (t80) REVERT: B 369 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8113 (mmtm) REVERT: B 376 ASP cc_start: 0.8480 (p0) cc_final: 0.8256 (p0) REVERT: B 383 GLN cc_start: 0.8109 (tp40) cc_final: 0.7820 (tp40) REVERT: B 384 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7259 (mm-30) REVERT: B 413 GLN cc_start: 0.7850 (pt0) cc_final: 0.7533 (tm-30) REVERT: B 422 VAL cc_start: 0.8509 (t) cc_final: 0.8251 (m) REVERT: B 426 ILE cc_start: 0.8818 (mt) cc_final: 0.8512 (tp) REVERT: B 432 MET cc_start: 0.7838 (tpt) cc_final: 0.7466 (tpt) REVERT: B 435 ILE cc_start: 0.9015 (mt) cc_final: 0.8783 (tp) REVERT: B 447 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8550 (mtpp) REVERT: B 470 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7437 (tpp80) REVERT: B 486 CYS cc_start: 0.8443 (t) cc_final: 0.8197 (t) REVERT: B 496 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8500 (mm) REVERT: B 507 LEU cc_start: 0.8494 (tp) cc_final: 0.8222 (tt) REVERT: B 530 TYR cc_start: 0.8139 (m-10) cc_final: 0.7898 (m-80) REVERT: B 537 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8286 (ttmm) REVERT: B 580 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8350 (mmtm) REVERT: B 668 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7506 (tp) REVERT: B 677 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7559 (ttm-80) REVERT: B 678 MET cc_start: 0.7293 (tpp) cc_final: 0.6854 (tpp) REVERT: B 681 LYS cc_start: 0.9013 (tptt) cc_final: 0.8458 (mmmm) REVERT: B 698 ASP cc_start: 0.7780 (t0) cc_final: 0.7369 (t70) REVERT: B 701 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 714 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7565 (mtt90) REVERT: B 731 ASN cc_start: 0.7811 (p0) cc_final: 0.7560 (p0) REVERT: B 732 GLN cc_start: 0.8230 (tt0) cc_final: 0.7591 (tm-30) outliers start: 53 outliers final: 37 residues processed: 354 average time/residue: 0.2708 time to fit residues: 130.8419 Evaluate side-chains 376 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 377 TYR 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 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 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 405 THR 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 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10400 Z= 0.211 Angle : 0.701 13.540 14136 Z= 0.355 Chirality : 0.043 0.188 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.333 50.783 1432 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.55 % Allowed : 20.05 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1322 helix: 1.09 (0.18), residues: 818 sheet: -1.61 (0.88), residues: 36 loop : -1.77 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 83 HIS 0.019 0.003 HIS A 375 PHE 0.024 0.001 PHE A 354 TYR 0.043 0.002 TYR A 361 ARG 0.013 0.001 ARG B 39 *********************** 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 379 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 328 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7988 (mmtt) REVERT: A 96 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8762 (mm) REVERT: A 97 VAL cc_start: 0.9024 (t) cc_final: 0.8726 (p) REVERT: A 122 PHE cc_start: 0.8122 (m-80) cc_final: 0.7704 (m-80) REVERT: A 145 SER cc_start: 0.8456 (m) cc_final: 0.8136 (p) REVERT: A 160 HIS cc_start: 0.6894 (t-90) cc_final: 0.6591 (t-90) REVERT: A 161 PHE cc_start: 0.7566 (m-80) cc_final: 0.6973 (m-80) REVERT: A 193 THR cc_start: 0.8565 (m) cc_final: 0.8279 (p) REVERT: A 200 GLN cc_start: 0.8144 (tt0) cc_final: 0.7809 (tt0) REVERT: A 235 GLN cc_start: 0.7704 (mm110) cc_final: 0.7497 (mm-40) REVERT: A 238 ILE cc_start: 0.8621 (mt) cc_final: 0.8389 (mt) REVERT: A 258 ILE cc_start: 0.8828 (tp) cc_final: 0.8546 (pt) REVERT: A 283 MET cc_start: 0.7511 (tpp) cc_final: 0.6640 (mpp) REVERT: A 286 LYS cc_start: 0.8988 (pttp) cc_final: 0.8574 (pttp) REVERT: A 293 LYS cc_start: 0.8803 (tppt) cc_final: 0.8455 (tppt) REVERT: A 361 TYR cc_start: 0.8638 (t80) cc_final: 0.8415 (t80) REVERT: A 384 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 394 PHE cc_start: 0.8376 (t80) cc_final: 0.7490 (t80) REVERT: A 421 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7768 (mm-40) REVERT: A 432 MET cc_start: 0.7653 (tpt) cc_final: 0.7335 (tpt) REVERT: A 435 ILE cc_start: 0.8969 (mt) cc_final: 0.8739 (tp) REVERT: A 459 LYS cc_start: 0.8931 (tppp) cc_final: 0.8569 (tppt) REVERT: A 470 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7594 (tpp80) REVERT: A 472 TRP cc_start: 0.8722 (t-100) cc_final: 0.8456 (t-100) REVERT: A 496 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8604 (mm) REVERT: A 519 ASN cc_start: 0.8112 (m110) cc_final: 0.7717 (m-40) REVERT: A 543 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 556 TYR cc_start: 0.8577 (p90) cc_final: 0.8281 (p90) REVERT: A 579 ASN cc_start: 0.8157 (p0) cc_final: 0.7560 (p0) REVERT: A 580 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8577 (mmtm) REVERT: A 677 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7561 (ttm-80) REVERT: A 681 LYS cc_start: 0.9045 (tptt) cc_final: 0.8547 (mmmm) REVERT: A 682 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 687 ASP cc_start: 0.8211 (t0) cc_final: 0.7750 (t0) REVERT: A 694 LEU cc_start: 0.8844 (mm) cc_final: 0.8461 (mt) REVERT: A 698 ASP cc_start: 0.7581 (t0) cc_final: 0.7379 (t0) REVERT: A 701 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 704 GLU cc_start: 0.7842 (tt0) cc_final: 0.7551 (tt0) REVERT: A 714 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7534 (mtt90) REVERT: A 732 GLN cc_start: 0.8280 (tt0) cc_final: 0.7579 (tm-30) REVERT: B 36 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.7538 (mmt-90) REVERT: B 37 GLU cc_start: 0.8036 (pp20) cc_final: 0.7683 (pp20) REVERT: B 39 ARG cc_start: 0.7298 (ttm110) cc_final: 0.7001 (mtp85) REVERT: B 46 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7118 (tm) REVERT: B 66 LYS cc_start: 0.8829 (tppt) cc_final: 0.8566 (tppt) REVERT: B 68 LEU cc_start: 0.8900 (tp) cc_final: 0.8609 (tp) REVERT: B 101 GLN cc_start: 0.8348 (tt0) cc_final: 0.7947 (tt0) REVERT: B 105 TYR cc_start: 0.8573 (m-80) cc_final: 0.8176 (m-80) REVERT: B 118 TYR cc_start: 0.7875 (m-10) cc_final: 0.7432 (m-80) REVERT: B 193 THR cc_start: 0.8752 (m) cc_final: 0.8476 (p) REVERT: B 203 PHE cc_start: 0.8062 (m-80) cc_final: 0.7603 (m-80) REVERT: B 211 ILE cc_start: 0.8369 (tt) cc_final: 0.7925 (pt) REVERT: B 240 LEU cc_start: 0.9176 (mt) cc_final: 0.8793 (tt) REVERT: B 286 LYS cc_start: 0.8890 (ptmt) cc_final: 0.8370 (ptmt) REVERT: B 287 GLU cc_start: 0.8300 (tp30) cc_final: 0.7492 (tp30) REVERT: B 292 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 355 SER cc_start: 0.8942 (m) cc_final: 0.8691 (p) REVERT: B 361 TYR cc_start: 0.8721 (t80) cc_final: 0.8407 (t80) REVERT: B 369 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8311 (mtmt) REVERT: B 383 GLN cc_start: 0.8118 (tp40) cc_final: 0.7835 (tp40) REVERT: B 384 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 413 GLN cc_start: 0.7773 (pt0) cc_final: 0.7406 (tm-30) REVERT: B 422 VAL cc_start: 0.8502 (t) cc_final: 0.8248 (m) REVERT: B 426 ILE cc_start: 0.8822 (mt) cc_final: 0.8507 (tp) REVERT: B 432 MET cc_start: 0.7847 (tpt) cc_final: 0.7428 (tpt) REVERT: B 435 ILE cc_start: 0.9023 (mt) cc_final: 0.8787 (tp) REVERT: B 447 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8510 (mtpp) REVERT: B 470 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7427 (tpp80) REVERT: B 486 CYS cc_start: 0.8449 (t) cc_final: 0.8199 (t) REVERT: B 496 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 507 LEU cc_start: 0.8504 (tp) cc_final: 0.8246 (tt) REVERT: B 537 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8291 (ttmm) REVERT: B 546 LYS cc_start: 0.8055 (tppt) cc_final: 0.7753 (tppt) REVERT: B 580 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8359 (mmtm) REVERT: B 668 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7822 (tp) REVERT: B 677 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7572 (ttm-80) REVERT: B 678 MET cc_start: 0.7292 (tpp) cc_final: 0.6846 (tpp) REVERT: B 681 LYS cc_start: 0.9078 (tptt) cc_final: 0.8573 (mmmm) REVERT: B 698 ASP cc_start: 0.7810 (t0) cc_final: 0.7398 (t70) REVERT: B 701 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 714 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7569 (mtt90) REVERT: B 732 GLN cc_start: 0.8182 (tt0) cc_final: 0.7689 (tm-30) outliers start: 51 outliers final: 39 residues processed: 355 average time/residue: 0.2519 time to fit residues: 119.8042 Evaluate side-chains 372 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 327 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR 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 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 385 PHE 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 496 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 350 LEU Chi-restraints excluded: chain B residue 405 THR 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 513 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.0050 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10400 Z= 0.213 Angle : 0.721 12.843 14136 Z= 0.367 Chirality : 0.044 0.294 1718 Planarity : 0.004 0.037 1758 Dihedral : 5.335 52.153 1431 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.46 % Allowed : 21.30 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1322 helix: 1.10 (0.18), residues: 820 sheet: -2.33 (0.71), residues: 48 loop : -1.73 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 83 HIS 0.019 0.002 HIS A 375 PHE 0.025 0.002 PHE B 394 TYR 0.037 0.002 TYR A 361 ARG 0.011 0.001 ARG B 39 *********************** 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 382 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 332 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: A 66 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8008 (mmtt) REVERT: A 96 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 97 VAL cc_start: 0.9024 (t) cc_final: 0.8716 (p) REVERT: A 145 SER cc_start: 0.8483 (m) cc_final: 0.8113 (p) REVERT: A 160 HIS cc_start: 0.6941 (t-90) cc_final: 0.6668 (t-90) REVERT: A 161 PHE cc_start: 0.7573 (m-80) cc_final: 0.7013 (m-80) REVERT: A 193 THR cc_start: 0.8546 (m) cc_final: 0.8272 (p) REVERT: A 200 GLN cc_start: 0.8135 (tt0) cc_final: 0.7837 (tt0) REVERT: A 235 GLN cc_start: 0.7618 (mm110) cc_final: 0.7408 (mm-40) REVERT: A 238 ILE cc_start: 0.8620 (mt) cc_final: 0.8384 (mt) REVERT: A 258 ILE cc_start: 0.8820 (tp) cc_final: 0.8541 (pt) REVERT: A 283 MET cc_start: 0.7462 (tpp) cc_final: 0.6559 (mpp) REVERT: A 286 LYS cc_start: 0.9006 (pttp) cc_final: 0.8587 (pttp) REVERT: A 293 LYS cc_start: 0.8795 (tppt) cc_final: 0.8460 (tppt) REVERT: A 361 TYR cc_start: 0.8643 (t80) cc_final: 0.8400 (t80) REVERT: A 384 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 394 PHE cc_start: 0.8381 (t80) cc_final: 0.8050 (t80) REVERT: A 432 MET cc_start: 0.7615 (tpt) cc_final: 0.7323 (tpt) REVERT: A 435 ILE cc_start: 0.8973 (mt) cc_final: 0.8755 (tp) REVERT: A 464 GLN cc_start: 0.8305 (tt0) cc_final: 0.7921 (tp40) REVERT: A 470 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 472 TRP cc_start: 0.8779 (t-100) cc_final: 0.8470 (t-100) REVERT: A 473 LYS cc_start: 0.8830 (mptt) cc_final: 0.8606 (mppt) REVERT: A 488 MET cc_start: 0.7690 (tpp) cc_final: 0.7474 (tpp) REVERT: A 496 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 519 ASN cc_start: 0.8109 (m110) cc_final: 0.7654 (m-40) REVERT: A 543 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 556 TYR cc_start: 0.8583 (p90) cc_final: 0.8236 (p90) REVERT: A 563 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8529 (tppp) REVERT: A 579 ASN cc_start: 0.8167 (p0) cc_final: 0.7646 (p0) REVERT: A 580 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8553 (mmtm) REVERT: A 677 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7556 (ttm-80) REVERT: A 681 LYS cc_start: 0.9029 (tptt) cc_final: 0.8512 (mmmm) REVERT: A 687 ASP cc_start: 0.8227 (t0) cc_final: 0.7918 (t0) REVERT: A 698 ASP cc_start: 0.7593 (t0) cc_final: 0.7383 (t0) REVERT: A 701 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 704 GLU cc_start: 0.7831 (tt0) cc_final: 0.7540 (tt0) REVERT: A 714 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7525 (mtt90) REVERT: A 732 GLN cc_start: 0.8312 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 36 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.7544 (mmt-90) REVERT: B 37 GLU cc_start: 0.8036 (pp20) cc_final: 0.7696 (pp20) REVERT: B 39 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7039 (mtp85) REVERT: B 46 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7117 (tm) REVERT: B 66 LYS cc_start: 0.8831 (tppt) cc_final: 0.8556 (tppt) REVERT: B 68 LEU cc_start: 0.8892 (tp) cc_final: 0.8600 (tp) REVERT: B 101 GLN cc_start: 0.8362 (tt0) cc_final: 0.7925 (tt0) REVERT: B 105 TYR cc_start: 0.8548 (m-80) cc_final: 0.8184 (m-80) REVERT: B 118 TYR cc_start: 0.7872 (m-10) cc_final: 0.7429 (m-80) REVERT: B 193 THR cc_start: 0.8748 (m) cc_final: 0.8466 (p) REVERT: B 203 PHE cc_start: 0.8048 (m-80) cc_final: 0.7565 (m-80) REVERT: B 211 ILE cc_start: 0.8365 (tt) cc_final: 0.7919 (pt) REVERT: B 240 LEU cc_start: 0.9190 (mt) cc_final: 0.8793 (tt) REVERT: B 286 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8397 (ptmt) REVERT: B 287 GLU cc_start: 0.8268 (tp30) cc_final: 0.7402 (tp30) REVERT: B 292 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6828 (t80) REVERT: B 355 SER cc_start: 0.8953 (m) cc_final: 0.8698 (p) REVERT: B 361 TYR cc_start: 0.8709 (t80) cc_final: 0.8402 (t80) REVERT: B 383 GLN cc_start: 0.8129 (tp40) cc_final: 0.7861 (tp40) REVERT: B 384 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 413 GLN cc_start: 0.7702 (pt0) cc_final: 0.7243 (tm-30) REVERT: B 422 VAL cc_start: 0.8469 (t) cc_final: 0.8218 (m) REVERT: B 426 ILE cc_start: 0.8819 (mt) cc_final: 0.8485 (tp) REVERT: B 432 MET cc_start: 0.7828 (tpt) cc_final: 0.7439 (tpt) REVERT: B 435 ILE cc_start: 0.9025 (mt) cc_final: 0.8807 (tp) REVERT: B 447 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8486 (mtpp) REVERT: B 464 GLN cc_start: 0.8507 (tt0) cc_final: 0.7695 (tp-100) REVERT: B 467 ASP cc_start: 0.7903 (p0) cc_final: 0.6417 (p0) REVERT: B 470 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7425 (tpp80) REVERT: B 486 CYS cc_start: 0.8439 (t) cc_final: 0.8184 (t) REVERT: B 496 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 503 LEU cc_start: 0.8942 (mm) cc_final: 0.8693 (mp) REVERT: B 507 LEU cc_start: 0.8493 (tp) cc_final: 0.8234 (tt) REVERT: B 546 LYS cc_start: 0.8048 (tppt) cc_final: 0.7737 (tppt) REVERT: B 580 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8368 (mmtm) REVERT: B 668 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (tp) REVERT: B 677 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7576 (ttm-80) REVERT: B 678 MET cc_start: 0.7304 (tpp) cc_final: 0.6885 (tpp) REVERT: B 681 LYS cc_start: 0.9079 (tptt) cc_final: 0.8574 (mmmm) REVERT: B 687 ASP cc_start: 0.8191 (t0) cc_final: 0.7760 (t0) REVERT: B 698 ASP cc_start: 0.7795 (t0) cc_final: 0.7379 (t70) REVERT: B 701 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 714 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7572 (mtt90) REVERT: B 732 GLN cc_start: 0.8326 (tt0) cc_final: 0.7603 (tm-30) outliers start: 50 outliers final: 36 residues processed: 361 average time/residue: 0.2401 time to fit residues: 116.7030 Evaluate side-chains 364 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR 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 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 350 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 462 PHE 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 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 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10400 Z= 0.250 Angle : 0.760 18.152 14136 Z= 0.389 Chirality : 0.045 0.244 1718 Planarity : 0.004 0.039 1758 Dihedral : 5.378 53.188 1431 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.01 % Allowed : 22.64 % Favored : 73.35 % 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: 1.01 (0.18), residues: 830 sheet: -2.21 (0.73), residues: 48 loop : -1.89 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 83 HIS 0.016 0.003 HIS B 728 PHE 0.025 0.002 PHE A 354 TYR 0.041 0.002 TYR A 361 ARG 0.011 0.001 ARG B 39 ********************** 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 377 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 332 time to evaluate : 1.068 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 66 LYS cc_start: 0.8520 (mmmt) cc_final: 0.7985 (mmtm) REVERT: A 96 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 97 VAL cc_start: 0.9065 (t) cc_final: 0.8777 (p) REVERT: A 121 PHE cc_start: 0.8049 (t80) cc_final: 0.7722 (t80) REVERT: A 145 SER cc_start: 0.8480 (m) cc_final: 0.8174 (p) REVERT: A 160 HIS cc_start: 0.6956 (t-90) cc_final: 0.6677 (t-90) REVERT: A 161 PHE cc_start: 0.7605 (m-80) cc_final: 0.7095 (m-80) REVERT: A 235 GLN cc_start: 0.7739 (mm110) cc_final: 0.7497 (mm-40) REVERT: A 238 ILE cc_start: 0.8643 (mt) cc_final: 0.8425 (mt) REVERT: A 258 ILE cc_start: 0.8832 (tp) cc_final: 0.8533 (pt) REVERT: A 283 MET cc_start: 0.7388 (tpp) cc_final: 0.7061 (mpp) REVERT: A 286 LYS cc_start: 0.8902 (pttp) cc_final: 0.8679 (ptmt) REVERT: A 293 LYS cc_start: 0.8792 (tppt) cc_final: 0.8492 (tppt) REVERT: A 384 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 394 PHE cc_start: 0.8406 (t80) cc_final: 0.7751 (t80) REVERT: A 432 MET cc_start: 0.7680 (tpt) cc_final: 0.7376 (tpt) REVERT: A 435 ILE cc_start: 0.9016 (mt) cc_final: 0.8814 (tp) REVERT: A 464 GLN cc_start: 0.8213 (tt0) cc_final: 0.7824 (tp40) REVERT: A 470 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7520 (tpp80) REVERT: A 473 LYS cc_start: 0.8849 (mptt) cc_final: 0.8632 (mppt) REVERT: A 488 MET cc_start: 0.7745 (tpp) cc_final: 0.7501 (tpp) REVERT: A 496 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 543 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 556 TYR cc_start: 0.8626 (p90) cc_final: 0.8382 (p90) REVERT: A 563 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8545 (tppp) REVERT: A 579 ASN cc_start: 0.8106 (p0) cc_final: 0.7544 (p0) REVERT: A 580 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8330 (mmtm) REVERT: A 583 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8625 (ptpt) REVERT: A 677 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7673 (tpp80) REVERT: A 681 LYS cc_start: 0.9023 (tptt) cc_final: 0.8559 (mmmm) REVERT: A 687 ASP cc_start: 0.8285 (t0) cc_final: 0.7985 (t0) REVERT: A 701 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 704 GLU cc_start: 0.7856 (tt0) cc_final: 0.7550 (tt0) REVERT: A 714 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7556 (mtt90) REVERT: A 732 GLN cc_start: 0.8337 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 36 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7546 (mmt-90) REVERT: B 37 GLU cc_start: 0.8013 (pp20) cc_final: 0.7694 (pp20) REVERT: B 46 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (tm) REVERT: B 68 LEU cc_start: 0.8904 (tp) cc_final: 0.8622 (tp) REVERT: B 101 GLN cc_start: 0.8402 (tt0) cc_final: 0.7799 (tt0) REVERT: B 105 TYR cc_start: 0.8564 (m-80) cc_final: 0.8184 (m-80) REVERT: B 118 TYR cc_start: 0.7884 (m-10) cc_final: 0.7344 (m-80) REVERT: B 122 PHE cc_start: 0.8134 (m-10) cc_final: 0.7919 (m-10) REVERT: B 128 PHE cc_start: 0.7758 (t80) cc_final: 0.7509 (t80) REVERT: B 130 PHE cc_start: 0.8059 (m-80) cc_final: 0.7852 (m-80) REVERT: B 193 THR cc_start: 0.8690 (m) cc_final: 0.8400 (p) REVERT: B 240 LEU cc_start: 0.9183 (mt) cc_final: 0.8799 (tt) REVERT: B 286 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8404 (ptmt) REVERT: B 287 GLU cc_start: 0.8248 (tp30) cc_final: 0.7376 (tp30) REVERT: B 292 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6813 (t80) REVERT: B 355 SER cc_start: 0.8941 (m) cc_final: 0.8691 (p) REVERT: B 361 TYR cc_start: 0.8690 (t80) cc_final: 0.8409 (t80) REVERT: B 383 GLN cc_start: 0.8182 (tp40) cc_final: 0.7917 (tp40) REVERT: B 384 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 413 GLN cc_start: 0.7709 (pt0) cc_final: 0.7345 (tm-30) REVERT: B 422 VAL cc_start: 0.8485 (t) cc_final: 0.8239 (m) REVERT: B 425 LEU cc_start: 0.8764 (mt) cc_final: 0.8558 (mm) REVERT: B 426 ILE cc_start: 0.8885 (mt) cc_final: 0.8490 (tp) REVERT: B 432 MET cc_start: 0.7856 (tpt) cc_final: 0.7402 (tpt) REVERT: B 435 ILE cc_start: 0.9069 (mt) cc_final: 0.8834 (tp) REVERT: B 447 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8520 (mtpp) REVERT: B 464 GLN cc_start: 0.8500 (tt0) cc_final: 0.7768 (tp-100) REVERT: B 467 ASP cc_start: 0.7994 (p0) cc_final: 0.6500 (p0) REVERT: B 470 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7437 (tpp80) REVERT: B 486 CYS cc_start: 0.8465 (t) cc_final: 0.8211 (t) REVERT: B 492 LEU cc_start: 0.8429 (mt) cc_final: 0.8222 (mt) REVERT: B 496 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8524 (mm) REVERT: B 507 LEU cc_start: 0.8538 (tp) cc_final: 0.8299 (tt) REVERT: B 541 GLU cc_start: 0.7241 (tp30) cc_final: 0.6973 (tp30) REVERT: B 580 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8406 (mmtm) REVERT: B 668 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 677 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7578 (ttm-80) REVERT: B 681 LYS cc_start: 0.9083 (tptt) cc_final: 0.8576 (mmmm) REVERT: B 682 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7509 (mt-10) REVERT: B 687 ASP cc_start: 0.8197 (t0) cc_final: 0.7784 (t0) REVERT: B 698 ASP cc_start: 0.7852 (t0) cc_final: 0.7443 (t70) REVERT: B 701 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 714 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7647 (mtt90) REVERT: B 732 GLN cc_start: 0.8442 (tt0) cc_final: 0.7657 (tm-30) outliers start: 45 outliers final: 37 residues processed: 358 average time/residue: 0.2487 time to fit residues: 119.5313 Evaluate side-chains 371 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 327 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR 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 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 583 LYS 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 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 496 LEU Chi-restraints excluded: chain B residue 513 VAL 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 96 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.0170 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 75 optimal weight: 0.3980 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094709 restraints weight = 22876.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098076 restraints weight = 11632.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100284 restraints weight = 7053.497| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10400 Z= 0.241 Angle : 0.775 17.274 14136 Z= 0.394 Chirality : 0.045 0.233 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.433 53.442 1429 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.92 % Allowed : 23.89 % Favored : 72.19 % 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: -0.05 (0.24), residues: 1322 helix: 1.00 (0.18), residues: 824 sheet: -2.17 (0.73), residues: 48 loop : -1.72 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 83 HIS 0.017 0.003 HIS A 728 PHE 0.045 0.002 PHE A 385 TYR 0.048 0.002 TYR A 361 ARG 0.014 0.001 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.10 seconds wall clock time: 50 minutes 52.88 seconds (3052.88 seconds total)