Starting phenix.real_space_refine on Wed Mar 4 02:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlb_32580/03_2026/7wlb_32580.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 6653 2.51 5 N 1687 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10193 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: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10193 At special positions: 0 Unit cell: (85.12, 127.68, 123.424, 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 1811 8.00 N 1687 7.00 C 6653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 468.6 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 64.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.774A pdb=" N GLN A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.860A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.617A 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: 5.183A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.063A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.894A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.603A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.852A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.613A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.665A 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 removed outlier: 3.811A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 376 removed outlier: 3.555A pdb=" N HIS A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.665A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.533A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.734A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.177A 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: 3.803A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.732A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.777A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.711A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.515A pdb=" N VAL A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.699A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.869A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.719A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.525A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.803A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.599A pdb=" N SER B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.587A pdb=" N LEU B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.774A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 removed outlier: 3.536A pdb=" N ALA B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 226 through 240 removed outlier: 4.161A 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: 3.647A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.527A pdb=" N ILE B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 370 removed outlier: 3.658A pdb=" N MET B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.596A pdb=" N THR B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.601A pdb=" N LEU B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.664A pdb=" N ALA B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 466 through 475 removed outlier: 3.992A pdb=" N ARG B 470 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.584A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.790A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 575 through 595 removed outlier: 3.570A pdb=" N ASN B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 700 through 706 removed outlier: 3.548A pdb=" N GLU B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.594A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.715A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 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 163 through 164 removed outlier: 4.010A pdb=" N VAL A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 175 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.712A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.445A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3212 1.35 - 1.46: 2296 1.46 - 1.58: 4823 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10395 Sorted by residual: bond pdb=" C THR B 224 " pdb=" N THR B 225 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.13e+00 bond pdb=" CA VAL A 111 " pdb=" CB VAL A 111 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.97e-01 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.85e-01 bond pdb=" C GLU B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.79e-01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 13733 1.11 - 2.21: 303 2.21 - 3.32: 63 3.32 - 4.43: 19 4.43 - 5.53: 10 Bond angle restraints: 14128 Sorted by residual: angle pdb=" N ARG A 134 " pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 114.56 111.35 3.21 1.27e+00 6.20e-01 6.38e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.31e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.65 -4.31 2.08e+00 2.31e-01 4.29e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 125.64 -3.67 1.80e+00 3.09e-01 4.15e+00 angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 121.97 125.59 -3.62 1.80e+00 3.09e-01 4.04e+00 ... (remaining 14123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 5960 16.92 - 33.83: 175 33.83 - 50.75: 40 50.75 - 67.67: 1 67.67 - 84.59: 4 Dihedral angle restraints: 6180 sinusoidal: 2353 harmonic: 3827 Sorted by residual: dihedral pdb=" CA LEU B 695 " pdb=" C LEU B 695 " pdb=" N GLN B 696 " pdb=" CA GLN B 696 " ideal model delta harmonic sigma weight residual -180.00 -164.38 -15.62 0 5.00e+00 4.00e-02 9.76e+00 dihedral pdb=" CB GLU B 259 " pdb=" CG GLU B 259 " pdb=" CD GLU B 259 " pdb=" OE1 GLU B 259 " ideal model delta sinusoidal sigma weight residual 0.00 84.59 -84.59 1 3.00e+01 1.11e-03 9.66e+00 dihedral pdb=" N ARG B 43 " pdb=" CA ARG B 43 " pdb=" CB ARG B 43 " pdb=" CG ARG B 43 " ideal model delta sinusoidal sigma weight residual -180.00 -128.33 -51.67 3 1.50e+01 4.44e-03 9.04e+00 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 963 0.026 - 0.051: 491 0.051 - 0.077: 179 0.077 - 0.103: 67 0.103 - 0.128: 16 Chirality restraints: 1716 Sorted by residual: 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 4.13e-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 3.96e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1713 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 76 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.020 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO B 654 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.017 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1026 2.74 - 3.28: 10986 3.28 - 3.82: 16738 3.82 - 4.36: 19313 4.36 - 4.90: 32636 Nonbonded interactions: 80699 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.284 3.040 ... (remaining 80694 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' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.044 10395 Z= 0.091 Angle : 0.445 5.533 14128 Z= 0.253 Chirality : 0.037 0.128 1716 Planarity : 0.003 0.042 1757 Dihedral : 8.675 84.585 3714 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.92 % Allowed : 5.70 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.19), residues: 1319 helix: -2.17 (0.15), residues: 815 sheet: -2.99 (0.81), residues: 32 loop : -3.43 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.005 0.001 TYR A 377 PHE 0.006 0.001 PHE A 115 TRP 0.004 0.000 TRP B 83 HIS 0.001 0.000 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00168 (10395) covalent geometry : angle 0.44474 (14128) hydrogen bonds : bond 0.24025 ( 546) hydrogen bonds : angle 6.82005 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 402 time to evaluate : 0.400 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8297 (ptt90) cc_final: 0.7243 (ptm-80) REVERT: A 66 LYS cc_start: 0.8672 (tppt) cc_final: 0.8421 (tppt) REVERT: A 96 LEU cc_start: 0.8897 (mt) cc_final: 0.8594 (mt) REVERT: A 97 VAL cc_start: 0.8489 (t) cc_final: 0.8285 (m) REVERT: A 114 GLN cc_start: 0.7501 (pt0) cc_final: 0.7108 (mp-120) REVERT: A 118 TYR cc_start: 0.7698 (m-10) cc_final: 0.7358 (m-80) REVERT: A 119 SER cc_start: 0.8507 (t) cc_final: 0.8171 (m) REVERT: A 121 PHE cc_start: 0.7481 (t80) cc_final: 0.7218 (t80) REVERT: A 161 PHE cc_start: 0.6960 (m-80) cc_final: 0.6281 (m-10) REVERT: A 230 GLN cc_start: 0.8786 (mt0) cc_final: 0.8234 (mt0) REVERT: A 232 LEU cc_start: 0.8587 (tp) cc_final: 0.8337 (tp) REVERT: A 251 LEU cc_start: 0.7706 (mt) cc_final: 0.6444 (mm) REVERT: A 252 SER cc_start: 0.8081 (p) cc_final: 0.7146 (m) REVERT: A 253 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8738 (tp) REVERT: A 255 TYR cc_start: 0.7779 (m-10) cc_final: 0.7334 (m-80) REVERT: A 259 GLU cc_start: 0.8242 (tt0) cc_final: 0.8031 (tt0) REVERT: A 263 ASN cc_start: 0.8826 (t0) cc_final: 0.8381 (t0) REVERT: A 272 PHE cc_start: 0.7816 (t80) cc_final: 0.7316 (t80) REVERT: A 286 LYS cc_start: 0.9080 (tppt) cc_final: 0.8435 (tppt) REVERT: A 289 ASN cc_start: 0.8116 (t0) cc_final: 0.7701 (t0) REVERT: A 305 ILE cc_start: 0.8563 (tp) cc_final: 0.8228 (pt) REVERT: A 306 VAL cc_start: 0.9028 (p) cc_final: 0.8683 (m) REVERT: A 309 ILE cc_start: 0.8736 (tp) cc_final: 0.8529 (pt) REVERT: A 314 SER cc_start: 0.8425 (t) cc_final: 0.8222 (p) REVERT: A 315 TYR cc_start: 0.7649 (t80) cc_final: 0.7348 (t80) REVERT: A 324 ASN cc_start: 0.7693 (t0) cc_final: 0.7218 (t0) REVERT: A 353 SER cc_start: 0.8949 (m) cc_final: 0.8642 (p) REVERT: A 369 LYS cc_start: 0.8638 (mmtt) cc_final: 0.7996 (mmtt) REVERT: A 371 TYR cc_start: 0.8386 (m-80) cc_final: 0.7783 (m-80) REVERT: A 382 ASN cc_start: 0.8752 (m110) cc_final: 0.8515 (m110) REVERT: A 385 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 390 ILE cc_start: 0.8682 (mt) cc_final: 0.8430 (tp) REVERT: A 392 ASN cc_start: 0.8923 (m-40) cc_final: 0.8485 (m-40) REVERT: A 394 PHE cc_start: 0.8007 (t80) cc_final: 0.7416 (t80) REVERT: A 409 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7477 (ttp-170) REVERT: A 413 GLN cc_start: 0.8392 (tt0) cc_final: 0.8179 (tt0) REVERT: A 432 MET cc_start: 0.8035 (tpt) cc_final: 0.7773 (tpt) REVERT: A 443 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 454 VAL cc_start: 0.8905 (t) cc_final: 0.8540 (p) REVERT: A 459 LYS cc_start: 0.8228 (tppp) cc_final: 0.6663 (tppp) REVERT: A 463 MET cc_start: 0.7641 (mmp) cc_final: 0.6629 (mmp) REVERT: A 473 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8153 (mtpt) REVERT: A 476 LYS cc_start: 0.8670 (mttm) cc_final: 0.8467 (mmtt) REVERT: A 477 THR cc_start: 0.7365 (p) cc_final: 0.6526 (p) REVERT: A 478 ASP cc_start: 0.7253 (m-30) cc_final: 0.6862 (m-30) REVERT: A 487 ILE cc_start: 0.8937 (mt) cc_final: 0.8728 (pt) REVERT: A 488 MET cc_start: 0.7572 (tpp) cc_final: 0.7164 (tpp) REVERT: A 496 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 512 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.7203 (tpp80) REVERT: A 560 ASP cc_start: 0.8164 (m-30) cc_final: 0.7895 (m-30) REVERT: A 563 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8135 (mmmt) REVERT: A 668 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7305 (tt) REVERT: A 674 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6823 (mtt180) REVERT: A 679 ILE cc_start: 0.8498 (mt) cc_final: 0.8144 (tp) REVERT: A 681 LYS cc_start: 0.8105 (tptt) cc_final: 0.7737 (tptt) REVERT: A 684 GLN cc_start: 0.8418 (tp40) cc_final: 0.7810 (tp40) REVERT: A 687 ASP cc_start: 0.8239 (t0) cc_final: 0.7811 (t0) REVERT: A 689 ASN cc_start: 0.7589 (m-40) cc_final: 0.6800 (m-40) REVERT: A 701 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 715 LYS cc_start: 0.8731 (mttm) cc_final: 0.8498 (mtpp) REVERT: A 723 HIS cc_start: 0.8330 (t-170) cc_final: 0.7548 (t-90) REVERT: A 727 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8171 (mt) REVERT: A 728 HIS cc_start: 0.8824 (t70) cc_final: 0.8381 (t70) REVERT: B 27 TYR cc_start: 0.8487 (m-10) cc_final: 0.7951 (m-10) REVERT: B 30 LEU cc_start: 0.8305 (pt) cc_final: 0.7988 (pt) REVERT: B 32 PHE cc_start: 0.8017 (t80) cc_final: 0.7770 (t80) REVERT: B 122 PHE cc_start: 0.7725 (m-80) cc_final: 0.7172 (m-80) REVERT: B 124 ILE cc_start: 0.8710 (mm) cc_final: 0.8483 (tp) REVERT: B 144 VAL cc_start: 0.8746 (p) cc_final: 0.8368 (m) REVERT: B 147 MET cc_start: 0.8784 (mtt) cc_final: 0.8478 (mtt) REVERT: B 192 LEU cc_start: 0.8990 (tp) cc_final: 0.8608 (tp) REVERT: B 196 VAL cc_start: 0.9074 (t) cc_final: 0.8833 (t) REVERT: B 199 ILE cc_start: 0.8076 (mp) cc_final: 0.7528 (tp) REVERT: B 203 PHE cc_start: 0.6522 (m-10) cc_final: 0.6096 (m-80) REVERT: B 230 GLN cc_start: 0.8441 (tp40) cc_final: 0.7854 (tp40) REVERT: B 233 VAL cc_start: 0.8978 (p) cc_final: 0.8644 (m) REVERT: B 235 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8161 (mm-40) REVERT: B 236 LEU cc_start: 0.8655 (tp) cc_final: 0.8400 (mt) REVERT: B 237 LYS cc_start: 0.8934 (pttt) cc_final: 0.8339 (pttp) REVERT: B 238 ILE cc_start: 0.8444 (tp) cc_final: 0.8235 (pt) REVERT: B 250 ILE cc_start: 0.8568 (pt) cc_final: 0.8234 (tp) REVERT: B 251 LEU cc_start: 0.8490 (mm) cc_final: 0.6387 (mm) REVERT: B 254 ILE cc_start: 0.8400 (mm) cc_final: 0.7908 (tp) REVERT: B 255 TYR cc_start: 0.7223 (m-10) cc_final: 0.6834 (m-80) REVERT: B 260 ILE cc_start: 0.9059 (mt) cc_final: 0.8803 (pt) REVERT: B 279 ILE cc_start: 0.8307 (tp) cc_final: 0.7423 (pt) REVERT: B 280 ILE cc_start: 0.8046 (mm) cc_final: 0.7823 (mm) REVERT: B 286 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8524 (mtmm) REVERT: B 318 ASN cc_start: 0.8162 (t0) cc_final: 0.7383 (t0) REVERT: B 319 LEU cc_start: 0.8635 (mt) cc_final: 0.8158 (mt) REVERT: B 321 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8089 (ttpp) REVERT: B 322 ASN cc_start: 0.7673 (m-40) cc_final: 0.7329 (t0) REVERT: B 323 TYR cc_start: 0.7811 (m-80) cc_final: 0.6768 (m-80) REVERT: B 324 ASN cc_start: 0.8128 (t0) cc_final: 0.7710 (t0) REVERT: B 359 VAL cc_start: 0.8794 (p) cc_final: 0.8550 (p) REVERT: B 455 ILE cc_start: 0.8529 (mt) cc_final: 0.7561 (mp) REVERT: B 459 LYS cc_start: 0.8726 (mmtt) cc_final: 0.7669 (mmtt) REVERT: B 461 MET cc_start: 0.8375 (mtt) cc_final: 0.8115 (mtp) REVERT: B 463 MET cc_start: 0.7077 (mmm) cc_final: 0.6120 (mmm) REVERT: B 473 LYS cc_start: 0.8430 (mttp) cc_final: 0.7950 (pttp) REVERT: B 484 PHE cc_start: 0.8262 (t80) cc_final: 0.7786 (t80) REVERT: B 486 CYS cc_start: 0.8531 (t) cc_final: 0.8278 (p) REVERT: B 488 MET cc_start: 0.7114 (tpp) cc_final: 0.6020 (tpp) REVERT: B 491 ILE cc_start: 0.8443 (mt) cc_final: 0.8111 (mt) REVERT: B 492 LEU cc_start: 0.8668 (mt) cc_final: 0.7245 (mt) REVERT: B 494 LEU cc_start: 0.8780 (mt) cc_final: 0.8523 (mm) REVERT: B 496 LEU cc_start: 0.8166 (mt) cc_final: 0.7036 (mt) REVERT: B 512 ARG cc_start: 0.8373 (mtm180) cc_final: 0.7810 (mtm-85) REVERT: B 514 GLN cc_start: 0.8596 (tt0) cc_final: 0.8001 (tm-30) REVERT: B 537 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7539 (mtmm) REVERT: B 576 ARG cc_start: 0.8217 (ptt90) cc_final: 0.7883 (ptt90) REVERT: B 577 VAL cc_start: 0.9173 (m) cc_final: 0.8910 (p) REVERT: B 578 TYR cc_start: 0.7680 (t80) cc_final: 0.5761 (t80) REVERT: B 580 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8342 (tttt) REVERT: B 585 LEU cc_start: 0.8910 (tp) cc_final: 0.8678 (tp) REVERT: B 655 ILE cc_start: 0.8253 (mt) cc_final: 0.7139 (mt) REVERT: B 678 MET cc_start: 0.7884 (mmm) cc_final: 0.7581 (mmm) REVERT: B 682 GLU cc_start: 0.8114 (tp30) cc_final: 0.7658 (tp30) REVERT: B 684 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8832 (tp40) REVERT: B 685 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7557 (mtm180) REVERT: B 713 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8221 (mt) REVERT: B 720 LEU cc_start: 0.8902 (mp) cc_final: 0.8544 (mt) REVERT: B 721 THR cc_start: 0.8432 (p) cc_final: 0.7565 (p) REVERT: B 724 ASP cc_start: 0.8454 (m-30) cc_final: 0.8167 (m-30) REVERT: B 730 GLN cc_start: 0.8679 (tt0) cc_final: 0.8445 (tt0) outliers start: 44 outliers final: 17 residues processed: 435 average time/residue: 0.1216 time to fit residues: 69.4119 Evaluate side-chains 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 268 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 421 GLN A 464 GLN A 567 ASN A 705 GLN B 160 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 464 GLN B 474 GLN B 684 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.119476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097014 restraints weight = 26054.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100593 restraints weight = 15508.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103122 restraints weight = 10375.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.104702 restraints weight = 7559.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106194 restraints weight = 5963.881| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10395 Z= 0.163 Angle : 0.625 11.157 14128 Z= 0.325 Chirality : 0.042 0.215 1716 Planarity : 0.005 0.049 1757 Dihedral : 3.420 17.496 1415 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.21), residues: 1319 helix: -0.58 (0.17), residues: 832 sheet: -2.24 (0.89), residues: 32 loop : -3.12 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 213 TYR 0.010 0.001 TYR B 377 PHE 0.025 0.001 PHE A 203 TRP 0.020 0.002 TRP B 74 HIS 0.003 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00338 (10395) covalent geometry : angle 0.62471 (14128) hydrogen bonds : bond 0.04428 ( 546) hydrogen bonds : angle 4.14388 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 38 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7637 (ttm110) REVERT: A 96 LEU cc_start: 0.8923 (mt) cc_final: 0.8589 (pp) REVERT: A 100 LEU cc_start: 0.8844 (mm) cc_final: 0.8541 (mm) REVERT: A 105 TYR cc_start: 0.8404 (m-80) cc_final: 0.8125 (m-80) REVERT: A 119 SER cc_start: 0.8758 (t) cc_final: 0.8006 (p) REVERT: A 121 PHE cc_start: 0.7740 (t80) cc_final: 0.7456 (t80) REVERT: A 198 ILE cc_start: 0.8537 (mt) cc_final: 0.8335 (tp) REVERT: A 211 ILE cc_start: 0.8768 (tt) cc_final: 0.8523 (tp) REVERT: A 230 GLN cc_start: 0.8926 (mt0) cc_final: 0.8394 (tp-100) REVERT: A 235 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8050 (mt0) REVERT: A 237 LYS cc_start: 0.8895 (pttm) cc_final: 0.8460 (pttm) REVERT: A 245 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7614 (mtmm) REVERT: A 251 LEU cc_start: 0.7954 (mt) cc_final: 0.6937 (mm) REVERT: A 252 SER cc_start: 0.7993 (p) cc_final: 0.7427 (m) REVERT: A 255 TYR cc_start: 0.8017 (m-10) cc_final: 0.7615 (m-10) REVERT: A 259 GLU cc_start: 0.8179 (tt0) cc_final: 0.7968 (tt0) REVERT: A 263 ASN cc_start: 0.8929 (t0) cc_final: 0.8636 (t0) REVERT: A 271 ASP cc_start: 0.7741 (m-30) cc_final: 0.7494 (m-30) REVERT: A 272 PHE cc_start: 0.7933 (t80) cc_final: 0.7533 (t80) REVERT: A 276 LEU cc_start: 0.8723 (pp) cc_final: 0.8493 (pp) REVERT: A 282 CYS cc_start: 0.8771 (t) cc_final: 0.8298 (p) REVERT: A 286 LYS cc_start: 0.9118 (tppt) cc_final: 0.8633 (tppt) REVERT: A 293 LYS cc_start: 0.8037 (tppt) cc_final: 0.7728 (tppt) REVERT: A 303 GLU cc_start: 0.8601 (pm20) cc_final: 0.8379 (pm20) REVERT: A 305 ILE cc_start: 0.8676 (tp) cc_final: 0.8379 (tp) REVERT: A 306 VAL cc_start: 0.8983 (p) cc_final: 0.8647 (m) REVERT: A 309 ILE cc_start: 0.8859 (tp) cc_final: 0.8560 (pt) REVERT: A 315 TYR cc_start: 0.8102 (t80) cc_final: 0.7819 (t80) REVERT: A 321 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8078 (ptmm) REVERT: A 324 ASN cc_start: 0.8192 (t0) cc_final: 0.7662 (t0) REVERT: A 336 LEU cc_start: 0.8682 (pt) cc_final: 0.8304 (pt) REVERT: A 349 MET cc_start: 0.7131 (mtm) cc_final: 0.6810 (mtm) REVERT: A 354 PHE cc_start: 0.8822 (t80) cc_final: 0.8593 (t80) REVERT: A 369 LYS cc_start: 0.8718 (mmtt) cc_final: 0.7938 (mmtt) REVERT: A 371 TYR cc_start: 0.8380 (m-80) cc_final: 0.7719 (m-80) REVERT: A 382 ASN cc_start: 0.8950 (m110) cc_final: 0.8707 (m110) REVERT: A 384 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 385 PHE cc_start: 0.8246 (t80) cc_final: 0.7343 (t80) REVERT: A 394 PHE cc_start: 0.8309 (t80) cc_final: 0.7563 (t80) REVERT: A 401 PHE cc_start: 0.7867 (p90) cc_final: 0.7454 (p90) REVERT: A 432 MET cc_start: 0.8113 (tpt) cc_final: 0.7745 (tpt) REVERT: A 438 LEU cc_start: 0.8722 (tt) cc_final: 0.8517 (tt) REVERT: A 443 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 458 LEU cc_start: 0.8678 (mt) cc_final: 0.8413 (mt) REVERT: A 459 LYS cc_start: 0.8523 (tppp) cc_final: 0.6414 (tppp) REVERT: A 463 MET cc_start: 0.7901 (mmp) cc_final: 0.6537 (mmp) REVERT: A 473 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8395 (mtpt) REVERT: A 476 LYS cc_start: 0.8864 (mttm) cc_final: 0.8557 (mmtt) REVERT: A 478 ASP cc_start: 0.8192 (m-30) cc_final: 0.7971 (m-30) REVERT: A 486 CYS cc_start: 0.8656 (t) cc_final: 0.8182 (p) REVERT: A 487 ILE cc_start: 0.9009 (mt) cc_final: 0.8626 (pt) REVERT: A 488 MET cc_start: 0.8027 (tpp) cc_final: 0.7805 (tpp) REVERT: A 496 LEU cc_start: 0.8512 (mm) cc_final: 0.8309 (tp) REVERT: A 514 GLN cc_start: 0.8388 (tt0) cc_final: 0.8097 (tt0) REVERT: A 530 TYR cc_start: 0.8352 (m-10) cc_final: 0.7963 (m-10) REVERT: A 537 LYS cc_start: 0.8631 (tttt) cc_final: 0.8299 (tttt) REVERT: A 549 ARG cc_start: 0.7678 (ttt90) cc_final: 0.6968 (tpp-160) REVERT: A 560 ASP cc_start: 0.8255 (m-30) cc_final: 0.8018 (m-30) REVERT: A 563 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8237 (mmmt) REVERT: A 564 LYS cc_start: 0.8818 (tppt) cc_final: 0.8376 (tppt) REVERT: A 671 VAL cc_start: 0.8407 (t) cc_final: 0.8188 (p) REVERT: A 677 ARG cc_start: 0.8393 (ptm160) cc_final: 0.8150 (ptm160) REVERT: A 681 LYS cc_start: 0.8071 (tptt) cc_final: 0.7666 (tptt) REVERT: A 682 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6238 (tm-30) REVERT: A 685 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7667 (mtm-85) REVERT: A 687 ASP cc_start: 0.8353 (t0) cc_final: 0.7969 (t0) REVERT: A 701 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 704 GLU cc_start: 0.7399 (tt0) cc_final: 0.7127 (tt0) REVERT: A 705 GLN cc_start: 0.8014 (mm110) cc_final: 0.6870 (mm-40) REVERT: A 715 LYS cc_start: 0.8608 (mttm) cc_final: 0.8358 (mttm) REVERT: A 724 ASP cc_start: 0.8439 (m-30) cc_final: 0.8057 (m-30) REVERT: A 727 LEU cc_start: 0.9050 (mm) cc_final: 0.8011 (mt) REVERT: A 728 HIS cc_start: 0.8865 (t70) cc_final: 0.8498 (t70) REVERT: A 731 ASN cc_start: 0.8349 (m110) cc_final: 0.8028 (m110) REVERT: B 27 TYR cc_start: 0.8609 (m-10) cc_final: 0.7838 (m-10) REVERT: B 37 GLU cc_start: 0.8018 (pp20) cc_final: 0.7553 (pp20) REVERT: B 38 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7963 (mmm-85) REVERT: B 122 PHE cc_start: 0.8033 (m-80) cc_final: 0.7494 (m-80) REVERT: B 124 ILE cc_start: 0.8632 (mm) cc_final: 0.8264 (pt) REVERT: B 125 LEU cc_start: 0.8757 (mt) cc_final: 0.8462 (mt) REVERT: B 144 VAL cc_start: 0.8652 (p) cc_final: 0.8315 (m) REVERT: B 147 MET cc_start: 0.8930 (mtt) cc_final: 0.8621 (mtt) REVERT: B 213 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7153 (mtp85) REVERT: B 230 GLN cc_start: 0.8455 (tp40) cc_final: 0.7763 (tp40) REVERT: B 233 VAL cc_start: 0.9097 (p) cc_final: 0.8680 (m) REVERT: B 236 LEU cc_start: 0.8816 (tp) cc_final: 0.8615 (mt) REVERT: B 237 LYS cc_start: 0.8848 (pttt) cc_final: 0.8349 (pttp) REVERT: B 238 ILE cc_start: 0.8669 (tp) cc_final: 0.8182 (pt) REVERT: B 250 ILE cc_start: 0.8614 (pt) cc_final: 0.8379 (tp) REVERT: B 251 LEU cc_start: 0.8551 (mm) cc_final: 0.6631 (mm) REVERT: B 254 ILE cc_start: 0.8515 (mm) cc_final: 0.7899 (tp) REVERT: B 255 TYR cc_start: 0.7557 (m-10) cc_final: 0.6866 (m-80) REVERT: B 319 LEU cc_start: 0.8678 (mt) cc_final: 0.8193 (pp) REVERT: B 323 TYR cc_start: 0.8035 (m-80) cc_final: 0.6955 (m-80) REVERT: B 324 ASN cc_start: 0.8397 (t0) cc_final: 0.8119 (t0) REVERT: B 359 VAL cc_start: 0.8819 (p) cc_final: 0.8599 (m) REVERT: B 446 GLN cc_start: 0.8290 (tt0) cc_final: 0.7830 (tt0) REVERT: B 455 ILE cc_start: 0.8573 (mt) cc_final: 0.7587 (mp) REVERT: B 459 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7603 (mmtt) REVERT: B 463 MET cc_start: 0.7065 (mmm) cc_final: 0.6137 (mmm) REVERT: B 477 THR cc_start: 0.8352 (m) cc_final: 0.8065 (p) REVERT: B 482 TRP cc_start: 0.8317 (t60) cc_final: 0.8105 (t60) REVERT: B 484 PHE cc_start: 0.8485 (t80) cc_final: 0.7860 (t80) REVERT: B 488 MET cc_start: 0.7717 (tpp) cc_final: 0.6544 (tpp) REVERT: B 491 ILE cc_start: 0.8856 (mt) cc_final: 0.8466 (mm) REVERT: B 492 LEU cc_start: 0.8709 (mt) cc_final: 0.7392 (mt) REVERT: B 494 LEU cc_start: 0.9073 (mt) cc_final: 0.8707 (mm) REVERT: B 495 ASP cc_start: 0.7431 (p0) cc_final: 0.6841 (p0) REVERT: B 496 LEU cc_start: 0.7971 (mt) cc_final: 0.7153 (mt) REVERT: B 512 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8236 (mtm-85) REVERT: B 514 GLN cc_start: 0.8950 (tt0) cc_final: 0.8433 (tm-30) REVERT: B 537 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7539 (mtmm) REVERT: B 563 LYS cc_start: 0.9027 (tppt) cc_final: 0.8056 (tppt) REVERT: B 567 ASN cc_start: 0.8128 (m-40) cc_final: 0.7028 (m110) REVERT: B 580 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8479 (mmmt) REVERT: B 583 LYS cc_start: 0.8667 (pttp) cc_final: 0.8379 (ptmm) REVERT: B 666 SER cc_start: 0.8674 (p) cc_final: 0.8370 (p) REVERT: B 677 ARG cc_start: 0.8610 (ttt180) cc_final: 0.7958 (ttm-80) REVERT: B 678 MET cc_start: 0.8128 (mmm) cc_final: 0.7748 (mmm) REVERT: B 682 GLU cc_start: 0.8430 (tp30) cc_final: 0.7970 (tp30) REVERT: B 684 GLN cc_start: 0.9183 (tp40) cc_final: 0.8816 (tp40) REVERT: B 702 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7590 (tptp) REVERT: B 705 GLN cc_start: 0.8417 (tt0) cc_final: 0.8154 (tt0) REVERT: B 716 ASP cc_start: 0.8121 (t0) cc_final: 0.7910 (p0) REVERT: B 720 LEU cc_start: 0.8942 (mp) cc_final: 0.8676 (mt) REVERT: B 727 LEU cc_start: 0.8903 (mt) cc_final: 0.8641 (mt) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.1151 time to fit residues: 57.5613 Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 289 ASN A 383 GLN A 457 ASN A 728 HIS B 289 ASN B 392 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.114574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091501 restraints weight = 26496.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095055 restraints weight = 15790.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097530 restraints weight = 10622.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099370 restraints weight = 7804.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100711 restraints weight = 6113.384| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10395 Z= 0.215 Angle : 0.648 10.254 14128 Z= 0.339 Chirality : 0.043 0.246 1716 Planarity : 0.005 0.087 1757 Dihedral : 3.792 21.488 1415 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1319 helix: -0.12 (0.17), residues: 835 sheet: -2.11 (0.84), residues: 41 loop : -2.86 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 440 TYR 0.023 0.002 TYR B 247 PHE 0.019 0.001 PHE A 115 TRP 0.021 0.001 TRP B 74 HIS 0.003 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00418 (10395) covalent geometry : angle 0.64756 (14128) hydrogen bonds : bond 0.04104 ( 546) hydrogen bonds : angle 4.07227 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.376 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: symmetry clash REVERT: A 66 LYS cc_start: 0.8828 (tppt) cc_final: 0.8465 (mmmt) REVERT: A 96 LEU cc_start: 0.8867 (mt) cc_final: 0.8563 (mm) REVERT: A 100 LEU cc_start: 0.8862 (mm) cc_final: 0.8659 (mm) REVERT: A 105 TYR cc_start: 0.8738 (m-80) cc_final: 0.8085 (m-80) REVERT: A 119 SER cc_start: 0.8808 (t) cc_final: 0.8266 (p) REVERT: A 161 PHE cc_start: 0.7933 (m-10) cc_final: 0.6825 (m-10) REVERT: A 198 ILE cc_start: 0.8552 (mt) cc_final: 0.8343 (tp) REVERT: A 211 ILE cc_start: 0.8987 (tt) cc_final: 0.8656 (tp) REVERT: A 230 GLN cc_start: 0.8922 (mt0) cc_final: 0.8398 (tp-100) REVERT: A 235 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8300 (mm-40) REVERT: A 237 LYS cc_start: 0.8935 (pttp) cc_final: 0.8629 (pttm) REVERT: A 240 LEU cc_start: 0.8720 (mm) cc_final: 0.8515 (mp) REVERT: A 252 SER cc_start: 0.8195 (p) cc_final: 0.7726 (m) REVERT: A 262 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 263 ASN cc_start: 0.9112 (t0) cc_final: 0.8704 (t0) REVERT: A 272 PHE cc_start: 0.8122 (t80) cc_final: 0.7846 (t80) REVERT: A 276 LEU cc_start: 0.8765 (pp) cc_final: 0.8489 (pp) REVERT: A 279 ILE cc_start: 0.9185 (mm) cc_final: 0.8961 (mm) REVERT: A 285 VAL cc_start: 0.8700 (m) cc_final: 0.8196 (p) REVERT: A 286 LYS cc_start: 0.9141 (tppt) cc_final: 0.8670 (tppt) REVERT: A 293 LYS cc_start: 0.8156 (tppt) cc_final: 0.7788 (tppt) REVERT: A 305 ILE cc_start: 0.8721 (tp) cc_final: 0.8451 (tp) REVERT: A 306 VAL cc_start: 0.8931 (p) cc_final: 0.8569 (m) REVERT: A 309 ILE cc_start: 0.8950 (tp) cc_final: 0.8664 (pt) REVERT: A 321 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8139 (ttpp) REVERT: A 322 ASN cc_start: 0.8286 (m-40) cc_final: 0.7990 (m110) REVERT: A 324 ASN cc_start: 0.8332 (t0) cc_final: 0.7905 (t0) REVERT: A 345 LEU cc_start: 0.8494 (mt) cc_final: 0.7668 (mp) REVERT: A 349 MET cc_start: 0.7253 (mtm) cc_final: 0.6888 (mtm) REVERT: A 353 SER cc_start: 0.9047 (m) cc_final: 0.8717 (p) REVERT: A 369 LYS cc_start: 0.8803 (mmtt) cc_final: 0.7992 (mmtt) REVERT: A 371 TYR cc_start: 0.8346 (m-80) cc_final: 0.7768 (m-80) REVERT: A 385 PHE cc_start: 0.8292 (t80) cc_final: 0.7531 (t80) REVERT: A 392 ASN cc_start: 0.9259 (m-40) cc_final: 0.8892 (m-40) REVERT: A 394 PHE cc_start: 0.8378 (t80) cc_final: 0.7669 (t80) REVERT: A 397 PHE cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: A 401 PHE cc_start: 0.7994 (p90) cc_final: 0.7753 (p90) REVERT: A 432 MET cc_start: 0.8293 (tpt) cc_final: 0.7998 (tpt) REVERT: A 443 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 454 VAL cc_start: 0.8986 (t) cc_final: 0.8732 (t) REVERT: A 459 LYS cc_start: 0.8491 (tppp) cc_final: 0.6678 (tppp) REVERT: A 461 MET cc_start: 0.8878 (mtm) cc_final: 0.8572 (ptp) REVERT: A 463 MET cc_start: 0.7979 (mmp) cc_final: 0.6753 (mmp) REVERT: A 470 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7657 (ptt-90) REVERT: A 473 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8457 (mtpt) REVERT: A 476 LYS cc_start: 0.8876 (mttm) cc_final: 0.8563 (mmtt) REVERT: A 478 ASP cc_start: 0.8250 (m-30) cc_final: 0.8029 (m-30) REVERT: A 488 MET cc_start: 0.8053 (tpp) cc_final: 0.7646 (tpp) REVERT: A 496 LEU cc_start: 0.8778 (mm) cc_final: 0.8437 (tp) REVERT: A 514 GLN cc_start: 0.8318 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 530 TYR cc_start: 0.8412 (m-10) cc_final: 0.7992 (m-10) REVERT: A 537 LYS cc_start: 0.8646 (tttt) cc_final: 0.8220 (tttt) REVERT: A 540 GLU cc_start: 0.7660 (pt0) cc_final: 0.7008 (pm20) REVERT: A 549 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7259 (tpp-160) REVERT: A 560 ASP cc_start: 0.8264 (m-30) cc_final: 0.8017 (m-30) REVERT: A 563 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8317 (mmmt) REVERT: A 564 LYS cc_start: 0.8855 (tppt) cc_final: 0.8396 (tppt) REVERT: A 677 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8083 (ptm160) REVERT: A 681 LYS cc_start: 0.8160 (tptt) cc_final: 0.7863 (tptt) REVERT: A 687 ASP cc_start: 0.8473 (t0) cc_final: 0.8074 (t0) REVERT: A 689 ASN cc_start: 0.7844 (m-40) cc_final: 0.6942 (m-40) REVERT: A 691 TYR cc_start: 0.7475 (m-10) cc_final: 0.7162 (m-10) REVERT: A 697 ASP cc_start: 0.8616 (m-30) cc_final: 0.7071 (t0) REVERT: A 701 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 705 GLN cc_start: 0.8069 (mm110) cc_final: 0.7839 (tp-100) REVERT: A 715 LYS cc_start: 0.8510 (mttm) cc_final: 0.8078 (mttm) REVERT: A 723 HIS cc_start: 0.8343 (t70) cc_final: 0.8069 (t-90) REVERT: A 724 ASP cc_start: 0.8479 (m-30) cc_final: 0.8237 (m-30) REVERT: A 727 LEU cc_start: 0.8959 (mm) cc_final: 0.7914 (mt) REVERT: A 728 HIS cc_start: 0.8797 (t-90) cc_final: 0.8581 (t70) REVERT: A 730 GLN cc_start: 0.8457 (pp30) cc_final: 0.8221 (pp30) REVERT: A 731 ASN cc_start: 0.8598 (m110) cc_final: 0.7943 (m110) REVERT: B 27 TYR cc_start: 0.8766 (m-10) cc_final: 0.8026 (m-10) REVERT: B 37 GLU cc_start: 0.8315 (pp20) cc_final: 0.7863 (pp20) REVERT: B 38 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: B 105 TYR cc_start: 0.7471 (m-80) cc_final: 0.6944 (m-80) REVERT: B 122 PHE cc_start: 0.8148 (m-80) cc_final: 0.7641 (m-80) REVERT: B 124 ILE cc_start: 0.8679 (mm) cc_final: 0.8232 (pt) REVERT: B 125 LEU cc_start: 0.8805 (mt) cc_final: 0.8473 (mt) REVERT: B 144 VAL cc_start: 0.8654 (p) cc_final: 0.8114 (m) REVERT: B 147 MET cc_start: 0.9030 (mtt) cc_final: 0.8720 (mtt) REVERT: B 199 ILE cc_start: 0.8522 (tp) cc_final: 0.8307 (tp) REVERT: B 207 GLN cc_start: 0.8815 (tt0) cc_final: 0.8514 (tm-30) REVERT: B 213 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7031 (mtp180) REVERT: B 230 GLN cc_start: 0.8425 (tp40) cc_final: 0.7864 (tp40) REVERT: B 236 LEU cc_start: 0.8852 (tp) cc_final: 0.8373 (tp) REVERT: B 237 LYS cc_start: 0.9075 (pttt) cc_final: 0.8342 (pttp) REVERT: B 238 ILE cc_start: 0.8669 (tp) cc_final: 0.8251 (pt) REVERT: B 241 ASN cc_start: 0.8067 (m110) cc_final: 0.7495 (m110) REVERT: B 250 ILE cc_start: 0.8725 (pt) cc_final: 0.8451 (tp) REVERT: B 251 LEU cc_start: 0.8705 (mm) cc_final: 0.6660 (mm) REVERT: B 254 ILE cc_start: 0.8543 (mm) cc_final: 0.8009 (tp) REVERT: B 255 TYR cc_start: 0.7505 (m-10) cc_final: 0.6885 (m-80) REVERT: B 259 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 279 ILE cc_start: 0.8641 (tp) cc_final: 0.8314 (pt) REVERT: B 283 MET cc_start: 0.8103 (ptp) cc_final: 0.7777 (ptp) REVERT: B 303 GLU cc_start: 0.8982 (mp0) cc_final: 0.8598 (pm20) REVERT: B 318 ASN cc_start: 0.8684 (t0) cc_final: 0.7827 (t0) REVERT: B 319 LEU cc_start: 0.8654 (mt) cc_final: 0.8289 (pp) REVERT: B 383 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8260 (mm-40) REVERT: B 455 ILE cc_start: 0.8750 (mt) cc_final: 0.8408 (mp) REVERT: B 459 LYS cc_start: 0.8663 (mmtt) cc_final: 0.7556 (mmtt) REVERT: B 463 MET cc_start: 0.7257 (mmm) cc_final: 0.6365 (mmm) REVERT: B 484 PHE cc_start: 0.8505 (t80) cc_final: 0.7896 (t80) REVERT: B 488 MET cc_start: 0.7841 (tpp) cc_final: 0.6606 (tpp) REVERT: B 491 ILE cc_start: 0.8960 (mt) cc_final: 0.8579 (mm) REVERT: B 492 LEU cc_start: 0.8723 (mt) cc_final: 0.7355 (mt) REVERT: B 494 LEU cc_start: 0.9135 (mt) cc_final: 0.8653 (tt) REVERT: B 496 LEU cc_start: 0.7955 (mt) cc_final: 0.7622 (mm) REVERT: B 512 ARG cc_start: 0.8671 (mtm180) cc_final: 0.8153 (mtm-85) REVERT: B 514 GLN cc_start: 0.8903 (tt0) cc_final: 0.8389 (tm-30) REVERT: B 535 HIS cc_start: 0.7800 (m-70) cc_final: 0.7314 (m-70) REVERT: B 537 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7766 (mtmt) REVERT: B 549 ARG cc_start: 0.8183 (ttt180) cc_final: 0.7973 (ttt90) REVERT: B 563 LYS cc_start: 0.9022 (tppt) cc_final: 0.8035 (tppt) REVERT: B 567 ASN cc_start: 0.8217 (m-40) cc_final: 0.7367 (m110) REVERT: B 576 ARG cc_start: 0.8328 (ptt90) cc_final: 0.8038 (ptt90) REVERT: B 577 VAL cc_start: 0.8977 (m) cc_final: 0.8716 (p) REVERT: B 580 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 656 HIS cc_start: 0.7203 (m90) cc_final: 0.6935 (m90) REVERT: B 674 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8043 (ttm110) REVERT: B 677 ARG cc_start: 0.8620 (ttt180) cc_final: 0.7996 (ttm-80) REVERT: B 678 MET cc_start: 0.8177 (mmm) cc_final: 0.7772 (mmm) REVERT: B 682 GLU cc_start: 0.8407 (tp30) cc_final: 0.7707 (tp30) REVERT: B 684 GLN cc_start: 0.9163 (tp40) cc_final: 0.8852 (tp40) REVERT: B 701 GLU cc_start: 0.7874 (mp0) cc_final: 0.7480 (mp0) REVERT: B 720 LEU cc_start: 0.9109 (mp) cc_final: 0.8717 (mt) REVERT: B 724 ASP cc_start: 0.8537 (m-30) cc_final: 0.8147 (m-30) REVERT: B 727 LEU cc_start: 0.8996 (mt) cc_final: 0.8675 (mt) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1136 time to fit residues: 58.0268 Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 567 ASN B 289 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.114033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091626 restraints weight = 26291.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094962 restraints weight = 15973.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097370 restraints weight = 10912.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099060 restraints weight = 8043.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100347 restraints weight = 6348.970| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10395 Z= 0.168 Angle : 0.617 9.376 14128 Z= 0.321 Chirality : 0.043 0.260 1716 Planarity : 0.004 0.070 1757 Dihedral : 3.933 23.518 1415 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1319 helix: 0.20 (0.18), residues: 826 sheet: -1.79 (1.01), residues: 34 loop : -2.52 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 440 TYR 0.023 0.001 TYR B 578 PHE 0.020 0.001 PHE B 385 TRP 0.019 0.001 TRP B 74 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00345 (10395) covalent geometry : angle 0.61697 (14128) hydrogen bonds : bond 0.03777 ( 546) hydrogen bonds : angle 3.95444 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.316 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8422 (t80) cc_final: 0.7910 (t80) REVERT: A 66 LYS cc_start: 0.8833 (tppt) cc_final: 0.8611 (tppt) REVERT: A 96 LEU cc_start: 0.8806 (mt) cc_final: 0.8473 (mm) REVERT: A 101 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7988 (mt0) REVERT: A 105 TYR cc_start: 0.8688 (m-80) cc_final: 0.8301 (m-80) REVERT: A 119 SER cc_start: 0.8896 (t) cc_final: 0.8325 (p) REVERT: A 121 PHE cc_start: 0.7763 (t80) cc_final: 0.7466 (t80) REVERT: A 161 PHE cc_start: 0.7864 (m-10) cc_final: 0.7302 (m-10) REVERT: A 211 ILE cc_start: 0.9043 (tt) cc_final: 0.8724 (tp) REVERT: A 230 GLN cc_start: 0.8937 (mt0) cc_final: 0.8259 (tm-30) REVERT: A 235 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8311 (mm-40) REVERT: A 237 LYS cc_start: 0.8931 (pttp) cc_final: 0.8494 (pttm) REVERT: A 252 SER cc_start: 0.8247 (p) cc_final: 0.7745 (m) REVERT: A 255 TYR cc_start: 0.8047 (m-10) cc_final: 0.7703 (m-10) REVERT: A 272 PHE cc_start: 0.8121 (t80) cc_final: 0.7773 (t80) REVERT: A 276 LEU cc_start: 0.8751 (pp) cc_final: 0.8473 (pp) REVERT: A 279 ILE cc_start: 0.9138 (mm) cc_final: 0.8831 (tp) REVERT: A 282 CYS cc_start: 0.8626 (p) cc_final: 0.7880 (p) REVERT: A 283 MET cc_start: 0.7977 (mmp) cc_final: 0.7489 (mmp) REVERT: A 285 VAL cc_start: 0.8696 (m) cc_final: 0.8214 (p) REVERT: A 286 LYS cc_start: 0.8985 (tppt) cc_final: 0.8642 (tppt) REVERT: A 289 ASN cc_start: 0.8865 (m110) cc_final: 0.8206 (m110) REVERT: A 293 LYS cc_start: 0.8325 (tppt) cc_final: 0.7849 (tppt) REVERT: A 305 ILE cc_start: 0.8704 (tp) cc_final: 0.8300 (pt) REVERT: A 306 VAL cc_start: 0.8880 (p) cc_final: 0.8517 (m) REVERT: A 309 ILE cc_start: 0.8936 (tp) cc_final: 0.8642 (pt) REVERT: A 321 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8164 (ptmm) REVERT: A 324 ASN cc_start: 0.8316 (t0) cc_final: 0.7869 (t0) REVERT: A 345 LEU cc_start: 0.8486 (mt) cc_final: 0.7651 (mt) REVERT: A 349 MET cc_start: 0.7151 (mtm) cc_final: 0.6830 (mtm) REVERT: A 353 SER cc_start: 0.9044 (m) cc_final: 0.8701 (p) REVERT: A 369 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8031 (mmtt) REVERT: A 371 TYR cc_start: 0.8325 (m-80) cc_final: 0.7696 (m-80) REVERT: A 382 ASN cc_start: 0.8936 (m110) cc_final: 0.8659 (t0) REVERT: A 385 PHE cc_start: 0.8202 (t80) cc_final: 0.7366 (t80) REVERT: A 392 ASN cc_start: 0.9249 (m-40) cc_final: 0.8911 (m-40) REVERT: A 394 PHE cc_start: 0.8357 (t80) cc_final: 0.7644 (t80) REVERT: A 397 PHE cc_start: 0.7859 (t80) cc_final: 0.7576 (t80) REVERT: A 409 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7764 (mtm180) REVERT: A 432 MET cc_start: 0.8264 (tpt) cc_final: 0.7952 (tpt) REVERT: A 443 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 454 VAL cc_start: 0.8999 (t) cc_final: 0.8756 (t) REVERT: A 458 LEU cc_start: 0.8863 (mt) cc_final: 0.8534 (mt) REVERT: A 459 LYS cc_start: 0.8517 (tppp) cc_final: 0.6570 (tppp) REVERT: A 463 MET cc_start: 0.7898 (mmp) cc_final: 0.6666 (mmp) REVERT: A 467 ASP cc_start: 0.7961 (p0) cc_final: 0.7718 (p0) REVERT: A 470 ARG cc_start: 0.8022 (ptp-170) cc_final: 0.7707 (ptt-90) REVERT: A 473 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8438 (mtpt) REVERT: A 476 LYS cc_start: 0.8727 (mttm) cc_final: 0.8399 (mmmt) REVERT: A 488 MET cc_start: 0.8098 (tpp) cc_final: 0.7641 (mpp) REVERT: A 496 LEU cc_start: 0.8803 (mm) cc_final: 0.8478 (tp) REVERT: A 514 GLN cc_start: 0.8266 (tt0) cc_final: 0.7721 (tm-30) REVERT: A 530 TYR cc_start: 0.8305 (m-10) cc_final: 0.7957 (m-10) REVERT: A 535 HIS cc_start: 0.7381 (m170) cc_final: 0.7151 (m170) REVERT: A 537 LYS cc_start: 0.8481 (tttt) cc_final: 0.8226 (tttt) REVERT: A 540 GLU cc_start: 0.7646 (pt0) cc_final: 0.7011 (pm20) REVERT: A 549 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7069 (tpp-160) REVERT: A 563 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8410 (mmmt) REVERT: A 564 LYS cc_start: 0.8860 (tppt) cc_final: 0.8369 (tppt) REVERT: A 590 LYS cc_start: 0.8486 (pptt) cc_final: 0.8263 (tmmt) REVERT: A 677 ARG cc_start: 0.8445 (ptm160) cc_final: 0.8106 (ptm160) REVERT: A 687 ASP cc_start: 0.8446 (t0) cc_final: 0.8070 (t0) REVERT: A 691 TYR cc_start: 0.7650 (m-10) cc_final: 0.7356 (m-10) REVERT: A 697 ASP cc_start: 0.8616 (m-30) cc_final: 0.7028 (t0) REVERT: A 701 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 715 LYS cc_start: 0.8374 (mttm) cc_final: 0.7894 (mttm) REVERT: A 724 ASP cc_start: 0.8395 (m-30) cc_final: 0.8070 (m-30) REVERT: B 27 TYR cc_start: 0.8808 (m-10) cc_final: 0.8150 (m-10) REVERT: B 37 GLU cc_start: 0.8271 (pp20) cc_final: 0.7927 (pp20) REVERT: B 38 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7893 (ttt90) REVERT: B 105 TYR cc_start: 0.7324 (m-80) cc_final: 0.6888 (m-80) REVERT: B 122 PHE cc_start: 0.8164 (m-80) cc_final: 0.7641 (m-80) REVERT: B 124 ILE cc_start: 0.8721 (mm) cc_final: 0.8336 (pt) REVERT: B 125 LEU cc_start: 0.8769 (mt) cc_final: 0.8483 (mt) REVERT: B 137 SER cc_start: 0.7797 (t) cc_final: 0.7419 (t) REVERT: B 144 VAL cc_start: 0.8658 (p) cc_final: 0.8183 (m) REVERT: B 147 MET cc_start: 0.9102 (mtt) cc_final: 0.8670 (mtt) REVERT: B 159 ASP cc_start: 0.8211 (p0) cc_final: 0.7570 (p0) REVERT: B 199 ILE cc_start: 0.8550 (tp) cc_final: 0.8332 (tp) REVERT: B 210 PHE cc_start: 0.6984 (p90) cc_final: 0.6617 (p90) REVERT: B 230 GLN cc_start: 0.8360 (tp40) cc_final: 0.7820 (tp40) REVERT: B 235 GLN cc_start: 0.8342 (pp30) cc_final: 0.8128 (pp30) REVERT: B 236 LEU cc_start: 0.8818 (tp) cc_final: 0.8535 (tp) REVERT: B 237 LYS cc_start: 0.8961 (pttt) cc_final: 0.8456 (pttp) REVERT: B 238 ILE cc_start: 0.8662 (tp) cc_final: 0.8242 (pt) REVERT: B 241 ASN cc_start: 0.8077 (m110) cc_final: 0.7544 (m110) REVERT: B 250 ILE cc_start: 0.8710 (pt) cc_final: 0.8469 (tp) REVERT: B 251 LEU cc_start: 0.8740 (mm) cc_final: 0.6755 (mm) REVERT: B 255 TYR cc_start: 0.7545 (m-10) cc_final: 0.6958 (m-80) REVERT: B 259 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 260 ILE cc_start: 0.9121 (mt) cc_final: 0.8771 (mt) REVERT: B 303 GLU cc_start: 0.8996 (mp0) cc_final: 0.8668 (pm20) REVERT: B 327 ILE cc_start: 0.7237 (pt) cc_final: 0.6898 (pt) REVERT: B 359 VAL cc_start: 0.8931 (p) cc_final: 0.8717 (m) REVERT: B 383 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8214 (mm-40) REVERT: B 443 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6893 (tm-30) REVERT: B 447 LYS cc_start: 0.9077 (mttt) cc_final: 0.8806 (ptpt) REVERT: B 455 ILE cc_start: 0.8684 (mt) cc_final: 0.8263 (mp) REVERT: B 459 LYS cc_start: 0.8740 (mmtt) cc_final: 0.7543 (mmtt) REVERT: B 463 MET cc_start: 0.7332 (mmm) cc_final: 0.6449 (mmm) REVERT: B 484 PHE cc_start: 0.8468 (t80) cc_final: 0.7878 (t80) REVERT: B 488 MET cc_start: 0.7793 (tpp) cc_final: 0.6503 (tpp) REVERT: B 491 ILE cc_start: 0.8960 (mt) cc_final: 0.8561 (mm) REVERT: B 492 LEU cc_start: 0.8696 (mt) cc_final: 0.7300 (mt) REVERT: B 494 LEU cc_start: 0.9146 (mt) cc_final: 0.8765 (mm) REVERT: B 496 LEU cc_start: 0.7958 (mt) cc_final: 0.7688 (mm) REVERT: B 512 ARG cc_start: 0.8606 (mtm180) cc_final: 0.8183 (mtm-85) REVERT: B 514 GLN cc_start: 0.8921 (tt0) cc_final: 0.8406 (tm-30) REVERT: B 517 SER cc_start: 0.8268 (p) cc_final: 0.7816 (p) REVERT: B 537 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7800 (mtmt) REVERT: B 563 LYS cc_start: 0.8998 (tppt) cc_final: 0.7900 (tppt) REVERT: B 567 ASN cc_start: 0.8190 (m-40) cc_final: 0.7373 (m110) REVERT: B 577 VAL cc_start: 0.8937 (m) cc_final: 0.8692 (p) REVERT: B 592 ILE cc_start: 0.8751 (mm) cc_final: 0.8523 (mm) REVERT: B 656 HIS cc_start: 0.7246 (m90) cc_final: 0.6979 (m90) REVERT: B 669 ASP cc_start: 0.7651 (p0) cc_final: 0.7104 (p0) REVERT: B 674 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8015 (ttm110) REVERT: B 677 ARG cc_start: 0.8570 (ttt180) cc_final: 0.7865 (ttm-80) REVERT: B 678 MET cc_start: 0.8216 (mmm) cc_final: 0.7824 (mmm) REVERT: B 682 GLU cc_start: 0.8223 (tp30) cc_final: 0.7491 (tp30) REVERT: B 684 GLN cc_start: 0.9158 (tp40) cc_final: 0.8842 (tp40) REVERT: B 716 ASP cc_start: 0.8164 (p0) cc_final: 0.7349 (t0) REVERT: B 719 PHE cc_start: 0.7756 (m-80) cc_final: 0.7396 (m-10) REVERT: B 720 LEU cc_start: 0.9138 (mp) cc_final: 0.8780 (mt) REVERT: B 724 ASP cc_start: 0.8521 (m-30) cc_final: 0.8179 (m-30) REVERT: B 727 LEU cc_start: 0.9028 (mt) cc_final: 0.8750 (mt) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1072 time to fit residues: 54.2745 Evaluate side-chains 338 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 128 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.114433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092256 restraints weight = 26223.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095575 restraints weight = 16013.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097914 restraints weight = 10969.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099610 restraints weight = 8120.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100732 restraints weight = 6421.364| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10395 Z= 0.137 Angle : 0.609 12.909 14128 Z= 0.311 Chirality : 0.043 0.407 1716 Planarity : 0.004 0.053 1757 Dihedral : 3.954 22.592 1415 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.23), residues: 1319 helix: 0.40 (0.18), residues: 813 sheet: -1.40 (1.01), residues: 33 loop : -2.41 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.011 0.001 TYR B 578 PHE 0.018 0.001 PHE B 385 TRP 0.020 0.001 TRP B 482 HIS 0.004 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00292 (10395) covalent geometry : angle 0.60927 (14128) hydrogen bonds : bond 0.03750 ( 546) hydrogen bonds : angle 3.78679 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.355 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: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8360 (t80) cc_final: 0.7922 (t80) REVERT: A 66 LYS cc_start: 0.8817 (tppt) cc_final: 0.8159 (tppt) REVERT: A 96 LEU cc_start: 0.8772 (mt) cc_final: 0.8432 (mm) REVERT: A 101 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8183 (mm110) REVERT: A 103 MET cc_start: 0.8245 (mtm) cc_final: 0.7706 (mtm) REVERT: A 105 TYR cc_start: 0.8599 (m-80) cc_final: 0.8246 (m-80) REVERT: A 119 SER cc_start: 0.8768 (t) cc_final: 0.8199 (p) REVERT: A 121 PHE cc_start: 0.7669 (t80) cc_final: 0.7367 (t80) REVERT: A 161 PHE cc_start: 0.7871 (m-10) cc_final: 0.7116 (m-10) REVERT: A 194 LEU cc_start: 0.8492 (tp) cc_final: 0.8192 (mm) REVERT: A 211 ILE cc_start: 0.9021 (tt) cc_final: 0.8686 (tp) REVERT: A 230 GLN cc_start: 0.8853 (mt0) cc_final: 0.8272 (tp40) REVERT: A 235 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8263 (mm-40) REVERT: A 237 LYS cc_start: 0.8973 (pttp) cc_final: 0.8512 (pttm) REVERT: A 252 SER cc_start: 0.8201 (p) cc_final: 0.7695 (m) REVERT: A 255 TYR cc_start: 0.8001 (m-10) cc_final: 0.7625 (m-10) REVERT: A 259 GLU cc_start: 0.8416 (tt0) cc_final: 0.7974 (tt0) REVERT: A 272 PHE cc_start: 0.8083 (t80) cc_final: 0.7742 (t80) REVERT: A 276 LEU cc_start: 0.8752 (pp) cc_final: 0.8442 (pp) REVERT: A 279 ILE cc_start: 0.9121 (mm) cc_final: 0.8779 (mm) REVERT: A 282 CYS cc_start: 0.8612 (p) cc_final: 0.8012 (p) REVERT: A 283 MET cc_start: 0.7970 (mmp) cc_final: 0.7426 (mmp) REVERT: A 285 VAL cc_start: 0.8706 (m) cc_final: 0.8224 (p) REVERT: A 286 LYS cc_start: 0.8930 (tppt) cc_final: 0.8638 (tppt) REVERT: A 289 ASN cc_start: 0.8884 (m110) cc_final: 0.8327 (m-40) REVERT: A 293 LYS cc_start: 0.8320 (tppt) cc_final: 0.7839 (tppt) REVERT: A 305 ILE cc_start: 0.8702 (tp) cc_final: 0.8261 (pt) REVERT: A 309 ILE cc_start: 0.8893 (tp) cc_final: 0.8602 (pt) REVERT: A 321 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8189 (ptmm) REVERT: A 324 ASN cc_start: 0.8182 (t0) cc_final: 0.7834 (t0) REVERT: A 329 LYS cc_start: 0.6353 (pttt) cc_final: 0.5636 (ttpp) REVERT: A 345 LEU cc_start: 0.8471 (mt) cc_final: 0.7676 (mt) REVERT: A 349 MET cc_start: 0.7015 (mtm) cc_final: 0.6655 (mtm) REVERT: A 353 SER cc_start: 0.9027 (m) cc_final: 0.8677 (p) REVERT: A 369 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8096 (mmtt) REVERT: A 371 TYR cc_start: 0.8327 (m-80) cc_final: 0.7758 (m-80) REVERT: A 385 PHE cc_start: 0.8139 (t80) cc_final: 0.7299 (t80) REVERT: A 392 ASN cc_start: 0.9239 (m-40) cc_final: 0.8886 (m-40) REVERT: A 394 PHE cc_start: 0.8302 (t80) cc_final: 0.7731 (t80) REVERT: A 397 PHE cc_start: 0.7819 (t80) cc_final: 0.7606 (t80) REVERT: A 414 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 432 MET cc_start: 0.8214 (tpt) cc_final: 0.7823 (tpt) REVERT: A 443 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 454 VAL cc_start: 0.9004 (t) cc_final: 0.8788 (t) REVERT: A 459 LYS cc_start: 0.8467 (tppp) cc_final: 0.6699 (tppp) REVERT: A 463 MET cc_start: 0.7944 (mmp) cc_final: 0.6736 (mmp) REVERT: A 467 ASP cc_start: 0.7912 (p0) cc_final: 0.7682 (p0) REVERT: A 470 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7739 (ptt-90) REVERT: A 473 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8434 (mtpt) REVERT: A 476 LYS cc_start: 0.8677 (mttm) cc_final: 0.8442 (mtpt) REVERT: A 488 MET cc_start: 0.8052 (tpp) cc_final: 0.7424 (mpp) REVERT: A 496 LEU cc_start: 0.8797 (mm) cc_final: 0.8490 (tp) REVERT: A 514 GLN cc_start: 0.8268 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 530 TYR cc_start: 0.8276 (m-10) cc_final: 0.7848 (m-80) REVERT: A 537 LYS cc_start: 0.8475 (tttt) cc_final: 0.8212 (tttt) REVERT: A 549 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7107 (tpp-160) REVERT: A 560 ASP cc_start: 0.8413 (m-30) cc_final: 0.8147 (m-30) REVERT: A 563 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8240 (mmmt) REVERT: A 564 LYS cc_start: 0.8866 (tppt) cc_final: 0.8441 (tppt) REVERT: A 687 ASP cc_start: 0.8427 (t0) cc_final: 0.8012 (t0) REVERT: A 697 ASP cc_start: 0.8673 (m-30) cc_final: 0.7728 (p0) REVERT: A 701 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 705 GLN cc_start: 0.7762 (tp40) cc_final: 0.7411 (tp-100) REVERT: A 715 LYS cc_start: 0.8305 (mttm) cc_final: 0.7747 (mttm) REVERT: A 724 ASP cc_start: 0.8414 (m-30) cc_final: 0.8075 (m-30) REVERT: A 728 HIS cc_start: 0.8812 (t70) cc_final: 0.8510 (t70) REVERT: A 731 ASN cc_start: 0.8468 (m110) cc_final: 0.8138 (m110) REVERT: B 27 TYR cc_start: 0.8771 (m-10) cc_final: 0.8113 (m-10) REVERT: B 30 LEU cc_start: 0.8524 (pt) cc_final: 0.8216 (pt) REVERT: B 37 GLU cc_start: 0.8209 (pp20) cc_final: 0.7884 (pp20) REVERT: B 38 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7876 (ttt90) REVERT: B 105 TYR cc_start: 0.7264 (m-80) cc_final: 0.6807 (m-80) REVERT: B 122 PHE cc_start: 0.8224 (m-80) cc_final: 0.7698 (m-80) REVERT: B 124 ILE cc_start: 0.8719 (mm) cc_final: 0.8299 (pt) REVERT: B 125 LEU cc_start: 0.8762 (mt) cc_final: 0.8474 (mt) REVERT: B 137 SER cc_start: 0.7834 (t) cc_final: 0.7523 (t) REVERT: B 144 VAL cc_start: 0.8585 (p) cc_final: 0.8116 (m) REVERT: B 147 MET cc_start: 0.9080 (mtt) cc_final: 0.8676 (mtt) REVERT: B 199 ILE cc_start: 0.8465 (tp) cc_final: 0.8231 (tp) REVERT: B 207 GLN cc_start: 0.8923 (tt0) cc_final: 0.8219 (tm-30) REVERT: B 236 LEU cc_start: 0.8709 (tp) cc_final: 0.8508 (tp) REVERT: B 237 LYS cc_start: 0.8953 (pttt) cc_final: 0.8169 (pttp) REVERT: B 238 ILE cc_start: 0.8665 (tp) cc_final: 0.8264 (pt) REVERT: B 241 ASN cc_start: 0.8165 (m110) cc_final: 0.7657 (m110) REVERT: B 247 TYR cc_start: 0.8102 (m-10) cc_final: 0.7875 (m-10) REVERT: B 250 ILE cc_start: 0.8718 (pt) cc_final: 0.8368 (mm) REVERT: B 251 LEU cc_start: 0.8612 (mm) cc_final: 0.6669 (mm) REVERT: B 255 TYR cc_start: 0.7625 (m-10) cc_final: 0.7034 (m-80) REVERT: B 259 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 260 ILE cc_start: 0.9077 (mt) cc_final: 0.8679 (mt) REVERT: B 271 ASP cc_start: 0.7947 (t70) cc_final: 0.7685 (t70) REVERT: B 279 ILE cc_start: 0.8745 (pt) cc_final: 0.8516 (tp) REVERT: B 290 ASP cc_start: 0.8359 (m-30) cc_final: 0.8104 (m-30) REVERT: B 303 GLU cc_start: 0.8986 (mp0) cc_final: 0.8626 (pm20) REVERT: B 318 ASN cc_start: 0.8325 (t0) cc_final: 0.7838 (t0) REVERT: B 321 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8308 (mtmt) REVERT: B 447 LYS cc_start: 0.9030 (mttt) cc_final: 0.8613 (mttt) REVERT: B 450 LEU cc_start: 0.7713 (tp) cc_final: 0.7507 (tp) REVERT: B 455 ILE cc_start: 0.8628 (mt) cc_final: 0.7904 (mp) REVERT: B 459 LYS cc_start: 0.8686 (mmtt) cc_final: 0.7512 (mmtt) REVERT: B 463 MET cc_start: 0.7259 (mmm) cc_final: 0.6374 (mmm) REVERT: B 467 ASP cc_start: 0.8494 (m-30) cc_final: 0.7967 (m-30) REVERT: B 473 LYS cc_start: 0.8348 (mttp) cc_final: 0.7577 (mttp) REVERT: B 477 THR cc_start: 0.8172 (m) cc_final: 0.7797 (p) REVERT: B 484 PHE cc_start: 0.8394 (t80) cc_final: 0.7806 (t80) REVERT: B 488 MET cc_start: 0.7736 (tpp) cc_final: 0.6385 (tpp) REVERT: B 491 ILE cc_start: 0.8928 (mt) cc_final: 0.8646 (mm) REVERT: B 492 LEU cc_start: 0.8663 (mt) cc_final: 0.7312 (mt) REVERT: B 494 LEU cc_start: 0.9166 (mt) cc_final: 0.8766 (mm) REVERT: B 496 LEU cc_start: 0.7945 (mt) cc_final: 0.7624 (mm) REVERT: B 512 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8160 (mtm-85) REVERT: B 514 GLN cc_start: 0.8873 (tt0) cc_final: 0.8398 (tm-30) REVERT: B 537 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7823 (mtmt) REVERT: B 563 LYS cc_start: 0.8983 (tppt) cc_final: 0.8130 (tppt) REVERT: B 577 VAL cc_start: 0.8950 (m) cc_final: 0.8663 (p) REVERT: B 578 TYR cc_start: 0.8258 (t80) cc_final: 0.7508 (t80) REVERT: B 580 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8445 (mmmt) REVERT: B 582 LEU cc_start: 0.8988 (mt) cc_final: 0.8709 (mm) REVERT: B 586 ARG cc_start: 0.8236 (ppt170) cc_final: 0.7906 (ttp80) REVERT: B 592 ILE cc_start: 0.8663 (mm) cc_final: 0.8386 (mm) REVERT: B 656 HIS cc_start: 0.7333 (m90) cc_final: 0.7057 (m90) REVERT: B 674 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8272 (ttm110) REVERT: B 677 ARG cc_start: 0.8530 (ttt180) cc_final: 0.7948 (ttm-80) REVERT: B 678 MET cc_start: 0.8169 (mmm) cc_final: 0.7829 (mmm) REVERT: B 682 GLU cc_start: 0.8201 (tp30) cc_final: 0.7497 (tp30) REVERT: B 705 GLN cc_start: 0.8454 (tt0) cc_final: 0.8133 (pp30) REVERT: B 716 ASP cc_start: 0.8204 (p0) cc_final: 0.7400 (t0) REVERT: B 720 LEU cc_start: 0.9114 (mp) cc_final: 0.8799 (mt) REVERT: B 727 LEU cc_start: 0.8988 (mt) cc_final: 0.7610 (mt) REVERT: B 730 GLN cc_start: 0.8891 (tt0) cc_final: 0.8394 (pp30) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1186 time to fit residues: 56.7570 Evaluate side-chains 330 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 375 HIS B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090310 restraints weight = 26630.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093676 restraints weight = 16222.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096084 restraints weight = 11105.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097704 restraints weight = 8189.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099004 restraints weight = 6498.982| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10395 Z= 0.165 Angle : 0.628 9.092 14128 Z= 0.323 Chirality : 0.043 0.293 1716 Planarity : 0.004 0.048 1757 Dihedral : 4.050 21.765 1415 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1319 helix: 0.46 (0.18), residues: 825 sheet: -1.37 (1.01), residues: 33 loop : -2.50 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 409 TYR 0.014 0.001 TYR B 377 PHE 0.024 0.001 PHE B 385 TRP 0.020 0.002 TRP B 482 HIS 0.006 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00337 (10395) covalent geometry : angle 0.62756 (14128) hydrogen bonds : bond 0.03786 ( 546) hydrogen bonds : angle 3.88687 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.383 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: A 20 TYR cc_start: 0.8412 (t80) cc_final: 0.8039 (t80) REVERT: A 38 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7558 (ttm110) REVERT: A 66 LYS cc_start: 0.8861 (tppt) cc_final: 0.8608 (tppt) REVERT: A 96 LEU cc_start: 0.8817 (mt) cc_final: 0.8462 (mm) REVERT: A 103 MET cc_start: 0.8426 (mtm) cc_final: 0.7771 (mtm) REVERT: A 119 SER cc_start: 0.8806 (t) cc_final: 0.8376 (p) REVERT: A 121 PHE cc_start: 0.7738 (t80) cc_final: 0.7352 (t80) REVERT: A 161 PHE cc_start: 0.7858 (m-10) cc_final: 0.6521 (m-10) REVERT: A 194 LEU cc_start: 0.8468 (tp) cc_final: 0.8160 (mm) REVERT: A 211 ILE cc_start: 0.9067 (tt) cc_final: 0.8728 (tp) REVERT: A 230 GLN cc_start: 0.8851 (mt0) cc_final: 0.8340 (tp-100) REVERT: A 234 SER cc_start: 0.9232 (m) cc_final: 0.8711 (p) REVERT: A 235 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8280 (mm-40) REVERT: A 237 LYS cc_start: 0.8966 (pttp) cc_final: 0.8496 (pttm) REVERT: A 252 SER cc_start: 0.8263 (p) cc_final: 0.7792 (m) REVERT: A 272 PHE cc_start: 0.8145 (t80) cc_final: 0.7818 (t80) REVERT: A 276 LEU cc_start: 0.8735 (pp) cc_final: 0.8445 (pp) REVERT: A 279 ILE cc_start: 0.9109 (mm) cc_final: 0.8829 (tp) REVERT: A 282 CYS cc_start: 0.8654 (p) cc_final: 0.8048 (p) REVERT: A 283 MET cc_start: 0.7987 (mmp) cc_final: 0.7393 (mmp) REVERT: A 285 VAL cc_start: 0.8748 (m) cc_final: 0.8271 (p) REVERT: A 286 LYS cc_start: 0.8927 (tppt) cc_final: 0.8638 (tppt) REVERT: A 289 ASN cc_start: 0.8925 (m110) cc_final: 0.8363 (m-40) REVERT: A 293 LYS cc_start: 0.8268 (tppt) cc_final: 0.7797 (tppt) REVERT: A 305 ILE cc_start: 0.8764 (tp) cc_final: 0.8322 (pt) REVERT: A 309 ILE cc_start: 0.8914 (tp) cc_final: 0.8611 (pt) REVERT: A 321 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8268 (ttpp) REVERT: A 324 ASN cc_start: 0.8287 (t0) cc_final: 0.7993 (t0) REVERT: A 329 LYS cc_start: 0.6479 (pttt) cc_final: 0.5960 (ttpp) REVERT: A 345 LEU cc_start: 0.8491 (mt) cc_final: 0.7630 (mt) REVERT: A 349 MET cc_start: 0.7107 (mtm) cc_final: 0.6634 (mtm) REVERT: A 353 SER cc_start: 0.8980 (m) cc_final: 0.8636 (p) REVERT: A 369 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8117 (mmtt) REVERT: A 371 TYR cc_start: 0.8295 (m-80) cc_final: 0.7671 (m-80) REVERT: A 385 PHE cc_start: 0.8158 (t80) cc_final: 0.7312 (t80) REVERT: A 392 ASN cc_start: 0.9263 (m-40) cc_final: 0.8885 (m-40) REVERT: A 394 PHE cc_start: 0.8327 (t80) cc_final: 0.7793 (t80) REVERT: A 397 PHE cc_start: 0.7853 (t80) cc_final: 0.7632 (t80) REVERT: A 414 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 432 MET cc_start: 0.8327 (tpt) cc_final: 0.7880 (tpt) REVERT: A 443 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 454 VAL cc_start: 0.9010 (t) cc_final: 0.8780 (t) REVERT: A 458 LEU cc_start: 0.8719 (mt) cc_final: 0.8464 (mt) REVERT: A 459 LYS cc_start: 0.8461 (tppp) cc_final: 0.6740 (tppp) REVERT: A 461 MET cc_start: 0.8956 (mtm) cc_final: 0.8675 (mtp) REVERT: A 463 MET cc_start: 0.8010 (mmp) cc_final: 0.6822 (mmp) REVERT: A 467 ASP cc_start: 0.7962 (p0) cc_final: 0.7707 (p0) REVERT: A 470 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7730 (ptt-90) REVERT: A 473 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8272 (mtpt) REVERT: A 476 LYS cc_start: 0.8765 (mttm) cc_final: 0.8437 (mmtt) REVERT: A 496 LEU cc_start: 0.8821 (mm) cc_final: 0.8496 (tt) REVERT: A 514 GLN cc_start: 0.8341 (tt0) cc_final: 0.7807 (tm-30) REVERT: A 530 TYR cc_start: 0.8258 (m-10) cc_final: 0.7871 (m-80) REVERT: A 535 HIS cc_start: 0.7444 (m170) cc_final: 0.7212 (m-70) REVERT: A 537 LYS cc_start: 0.8505 (tttt) cc_final: 0.8198 (tttt) REVERT: A 549 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7124 (tpp-160) REVERT: A 560 ASP cc_start: 0.8404 (m-30) cc_final: 0.8155 (m-30) REVERT: A 563 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8389 (mmmt) REVERT: A 564 LYS cc_start: 0.8897 (tppt) cc_final: 0.8453 (tppt) REVERT: A 590 LYS cc_start: 0.8543 (pptt) cc_final: 0.8259 (tmmt) REVERT: A 677 ARG cc_start: 0.8480 (ptm160) cc_final: 0.8223 (ptm160) REVERT: A 678 MET cc_start: 0.8120 (mmm) cc_final: 0.7701 (mmm) REVERT: A 687 ASP cc_start: 0.8459 (t0) cc_final: 0.8058 (t0) REVERT: A 697 ASP cc_start: 0.8654 (m-30) cc_final: 0.7755 (p0) REVERT: A 701 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 705 GLN cc_start: 0.7832 (tp40) cc_final: 0.7520 (tm-30) REVERT: A 715 LYS cc_start: 0.8311 (mttm) cc_final: 0.7765 (mttm) REVERT: A 724 ASP cc_start: 0.8440 (m-30) cc_final: 0.8151 (m-30) REVERT: A 727 LEU cc_start: 0.8831 (mm) cc_final: 0.8326 (mm) REVERT: A 728 HIS cc_start: 0.8842 (t70) cc_final: 0.8541 (t70) REVERT: A 731 ASN cc_start: 0.8561 (m110) cc_final: 0.8223 (m110) REVERT: B 27 TYR cc_start: 0.8828 (m-10) cc_final: 0.8177 (m-10) REVERT: B 32 PHE cc_start: 0.8424 (t80) cc_final: 0.8207 (t80) REVERT: B 33 GLN cc_start: 0.8407 (pp30) cc_final: 0.8081 (pp30) REVERT: B 37 GLU cc_start: 0.8227 (pp20) cc_final: 0.7640 (pp20) REVERT: B 38 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.7789 (ttt90) REVERT: B 105 TYR cc_start: 0.7320 (m-80) cc_final: 0.6981 (m-80) REVERT: B 122 PHE cc_start: 0.8280 (m-80) cc_final: 0.7723 (m-80) REVERT: B 124 ILE cc_start: 0.8765 (mm) cc_final: 0.8374 (pt) REVERT: B 125 LEU cc_start: 0.8784 (mt) cc_final: 0.8486 (mt) REVERT: B 137 SER cc_start: 0.7850 (t) cc_final: 0.7532 (t) REVERT: B 144 VAL cc_start: 0.8579 (p) cc_final: 0.8149 (m) REVERT: B 147 MET cc_start: 0.9108 (mtt) cc_final: 0.8709 (mtt) REVERT: B 199 ILE cc_start: 0.8505 (tp) cc_final: 0.8269 (tp) REVERT: B 207 GLN cc_start: 0.9011 (tt0) cc_final: 0.8346 (tm-30) REVERT: B 230 GLN cc_start: 0.8462 (pp30) cc_final: 0.7971 (pp30) REVERT: B 235 GLN cc_start: 0.8325 (pp30) cc_final: 0.8125 (pp30) REVERT: B 236 LEU cc_start: 0.8727 (tp) cc_final: 0.8443 (tp) REVERT: B 237 LYS cc_start: 0.8964 (pttt) cc_final: 0.8403 (pttp) REVERT: B 238 ILE cc_start: 0.8700 (tp) cc_final: 0.8303 (pt) REVERT: B 241 ASN cc_start: 0.8189 (m110) cc_final: 0.7712 (m-40) REVERT: B 247 TYR cc_start: 0.8127 (m-10) cc_final: 0.7824 (m-10) REVERT: B 250 ILE cc_start: 0.8734 (pt) cc_final: 0.8474 (tp) REVERT: B 251 LEU cc_start: 0.8592 (mm) cc_final: 0.6638 (mm) REVERT: B 255 TYR cc_start: 0.7597 (m-10) cc_final: 0.7025 (m-80) REVERT: B 259 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 260 ILE cc_start: 0.9083 (mt) cc_final: 0.8668 (mt) REVERT: B 271 ASP cc_start: 0.8061 (t70) cc_final: 0.7811 (t70) REVERT: B 286 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8574 (mtmm) REVERT: B 289 ASN cc_start: 0.8981 (m110) cc_final: 0.8742 (t0) REVERT: B 293 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8353 (mmtm) REVERT: B 303 GLU cc_start: 0.8996 (mp0) cc_final: 0.8609 (pm20) REVERT: B 447 LYS cc_start: 0.9001 (mttt) cc_final: 0.8768 (ptpp) REVERT: B 455 ILE cc_start: 0.8678 (mt) cc_final: 0.8106 (mm) REVERT: B 459 LYS cc_start: 0.8642 (mmtt) cc_final: 0.7495 (mmtt) REVERT: B 463 MET cc_start: 0.7303 (mmm) cc_final: 0.6400 (mmm) REVERT: B 467 ASP cc_start: 0.8524 (m-30) cc_final: 0.8111 (m-30) REVERT: B 473 LYS cc_start: 0.8381 (mttp) cc_final: 0.7645 (pttt) REVERT: B 476 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8359 (mmmt) REVERT: B 477 THR cc_start: 0.8156 (m) cc_final: 0.7792 (p) REVERT: B 484 PHE cc_start: 0.8404 (t80) cc_final: 0.7801 (t80) REVERT: B 488 MET cc_start: 0.7781 (tpp) cc_final: 0.6434 (tpp) REVERT: B 491 ILE cc_start: 0.8927 (mt) cc_final: 0.8541 (mm) REVERT: B 492 LEU cc_start: 0.8709 (mt) cc_final: 0.7269 (mt) REVERT: B 496 LEU cc_start: 0.7939 (mt) cc_final: 0.7658 (mm) REVERT: B 512 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8176 (mtm-85) REVERT: B 514 GLN cc_start: 0.8851 (tt0) cc_final: 0.8369 (tm-30) REVERT: B 537 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7758 (mtmm) REVERT: B 563 LYS cc_start: 0.8988 (tppt) cc_final: 0.8113 (tppt) REVERT: B 564 LYS cc_start: 0.9233 (ttmm) cc_final: 0.9007 (ttmm) REVERT: B 577 VAL cc_start: 0.8943 (m) cc_final: 0.8694 (p) REVERT: B 578 TYR cc_start: 0.8285 (t80) cc_final: 0.7541 (t80) REVERT: B 582 LEU cc_start: 0.8988 (mt) cc_final: 0.8686 (mm) REVERT: B 656 HIS cc_start: 0.7413 (m90) cc_final: 0.7126 (m90) REVERT: B 674 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8372 (ttm110) REVERT: B 677 ARG cc_start: 0.8583 (ttt180) cc_final: 0.7943 (ttm-80) REVERT: B 678 MET cc_start: 0.8196 (mmm) cc_final: 0.7828 (mmm) REVERT: B 682 GLU cc_start: 0.8249 (tp30) cc_final: 0.7533 (tp30) REVERT: B 691 TYR cc_start: 0.7635 (m-80) cc_final: 0.6912 (m-80) REVERT: B 716 ASP cc_start: 0.8201 (p0) cc_final: 0.7365 (t0) REVERT: B 719 PHE cc_start: 0.8158 (m-10) cc_final: 0.7956 (m-10) REVERT: B 720 LEU cc_start: 0.9164 (mp) cc_final: 0.8860 (mt) REVERT: B 727 LEU cc_start: 0.8978 (mt) cc_final: 0.7654 (mt) REVERT: B 730 GLN cc_start: 0.8916 (tt0) cc_final: 0.8432 (pp30) REVERT: B 731 ASN cc_start: 0.8450 (p0) cc_final: 0.7571 (p0) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1156 time to fit residues: 55.6963 Evaluate side-chains 335 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089443 restraints weight = 26390.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092736 restraints weight = 16099.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095040 restraints weight = 11027.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096721 restraints weight = 8181.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097969 restraints weight = 6480.211| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10395 Z= 0.178 Angle : 0.643 10.923 14128 Z= 0.333 Chirality : 0.045 0.409 1716 Planarity : 0.004 0.069 1757 Dihedral : 4.134 22.116 1415 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1319 helix: 0.47 (0.18), residues: 827 sheet: -1.66 (0.99), residues: 34 loop : -2.47 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 586 TYR 0.019 0.001 TYR A 105 PHE 0.026 0.001 PHE A 115 TRP 0.047 0.003 TRP B 482 HIS 0.003 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00363 (10395) covalent geometry : angle 0.64314 (14128) hydrogen bonds : bond 0.03835 ( 546) hydrogen bonds : angle 3.90494 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.387 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: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8446 (t80) cc_final: 0.8068 (t80) REVERT: A 29 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 38 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7611 (ttm110) REVERT: A 96 LEU cc_start: 0.8792 (mt) cc_final: 0.8428 (mm) REVERT: A 105 TYR cc_start: 0.8514 (m-80) cc_final: 0.8164 (m-80) REVERT: A 119 SER cc_start: 0.8777 (t) cc_final: 0.8269 (p) REVERT: A 121 PHE cc_start: 0.7731 (t80) cc_final: 0.7355 (t80) REVERT: A 161 PHE cc_start: 0.7877 (m-10) cc_final: 0.6486 (m-10) REVERT: A 194 LEU cc_start: 0.8450 (tp) cc_final: 0.8146 (mm) REVERT: A 211 ILE cc_start: 0.9064 (tt) cc_final: 0.8779 (tp) REVERT: A 230 GLN cc_start: 0.8871 (mt0) cc_final: 0.8105 (tm-30) REVERT: A 234 SER cc_start: 0.9190 (m) cc_final: 0.8583 (p) REVERT: A 235 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8304 (mm-40) REVERT: A 237 LYS cc_start: 0.9000 (pttp) cc_final: 0.8523 (pttm) REVERT: A 252 SER cc_start: 0.8320 (p) cc_final: 0.7861 (m) REVERT: A 272 PHE cc_start: 0.8122 (t80) cc_final: 0.7770 (t80) REVERT: A 276 LEU cc_start: 0.8737 (pp) cc_final: 0.8437 (pp) REVERT: A 279 ILE cc_start: 0.9124 (mm) cc_final: 0.8861 (tp) REVERT: A 281 VAL cc_start: 0.8863 (m) cc_final: 0.8634 (p) REVERT: A 282 CYS cc_start: 0.8595 (p) cc_final: 0.8037 (p) REVERT: A 283 MET cc_start: 0.7934 (mmp) cc_final: 0.7336 (mmp) REVERT: A 285 VAL cc_start: 0.8778 (m) cc_final: 0.8285 (p) REVERT: A 286 LYS cc_start: 0.8922 (tppt) cc_final: 0.8668 (tppt) REVERT: A 289 ASN cc_start: 0.8915 (m110) cc_final: 0.8311 (m110) REVERT: A 293 LYS cc_start: 0.8245 (tppt) cc_final: 0.7803 (tppt) REVERT: A 305 ILE cc_start: 0.8723 (tp) cc_final: 0.8315 (pt) REVERT: A 309 ILE cc_start: 0.8928 (tp) cc_final: 0.8635 (pt) REVERT: A 321 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8296 (ttpp) REVERT: A 329 LYS cc_start: 0.6480 (pttt) cc_final: 0.5934 (ttpp) REVERT: A 345 LEU cc_start: 0.8466 (mt) cc_final: 0.7608 (mt) REVERT: A 346 PHE cc_start: 0.8004 (m-10) cc_final: 0.7758 (m-10) REVERT: A 349 MET cc_start: 0.7086 (mtm) cc_final: 0.6599 (mtm) REVERT: A 353 SER cc_start: 0.8965 (m) cc_final: 0.8664 (p) REVERT: A 369 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8198 (mmtt) REVERT: A 371 TYR cc_start: 0.8306 (m-80) cc_final: 0.7691 (m-80) REVERT: A 382 ASN cc_start: 0.8848 (m110) cc_final: 0.8616 (t0) REVERT: A 385 PHE cc_start: 0.8162 (t80) cc_final: 0.7312 (t80) REVERT: A 392 ASN cc_start: 0.9250 (m-40) cc_final: 0.8909 (m-40) REVERT: A 394 PHE cc_start: 0.8330 (t80) cc_final: 0.7797 (t80) REVERT: A 397 PHE cc_start: 0.7852 (t80) cc_final: 0.7639 (t80) REVERT: A 414 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 432 MET cc_start: 0.8358 (tpt) cc_final: 0.7939 (tpt) REVERT: A 443 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 454 VAL cc_start: 0.9032 (t) cc_final: 0.8821 (t) REVERT: A 458 LEU cc_start: 0.8785 (mt) cc_final: 0.8482 (mt) REVERT: A 459 LYS cc_start: 0.8464 (tppp) cc_final: 0.6709 (tppp) REVERT: A 463 MET cc_start: 0.7966 (mmp) cc_final: 0.6780 (mmp) REVERT: A 467 ASP cc_start: 0.7940 (p0) cc_final: 0.7684 (p0) REVERT: A 470 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7723 (ptt-90) REVERT: A 473 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8331 (mtpt) REVERT: A 476 LYS cc_start: 0.8814 (mttm) cc_final: 0.8463 (mmtp) REVERT: A 496 LEU cc_start: 0.8836 (mm) cc_final: 0.8553 (tp) REVERT: A 514 GLN cc_start: 0.8387 (tt0) cc_final: 0.7899 (tm-30) REVERT: A 530 TYR cc_start: 0.8246 (m-10) cc_final: 0.7870 (m-10) REVERT: A 537 LYS cc_start: 0.8546 (tttt) cc_final: 0.8256 (tttt) REVERT: A 549 ARG cc_start: 0.7873 (ttt90) cc_final: 0.7003 (tpp-160) REVERT: A 560 ASP cc_start: 0.8415 (m-30) cc_final: 0.7981 (m-30) REVERT: A 563 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8355 (mmmt) REVERT: A 564 LYS cc_start: 0.8923 (tppt) cc_final: 0.8442 (tppt) REVERT: A 677 ARG cc_start: 0.8488 (ptm160) cc_final: 0.8279 (ptm160) REVERT: A 687 ASP cc_start: 0.8452 (t0) cc_final: 0.8040 (t0) REVERT: A 697 ASP cc_start: 0.8629 (m-30) cc_final: 0.7746 (p0) REVERT: A 701 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7483 (mm-30) REVERT: A 705 GLN cc_start: 0.7931 (tp40) cc_final: 0.7601 (tm-30) REVERT: A 724 ASP cc_start: 0.8373 (m-30) cc_final: 0.8084 (m-30) REVERT: A 727 LEU cc_start: 0.8822 (mm) cc_final: 0.8311 (mm) REVERT: A 728 HIS cc_start: 0.8826 (t70) cc_final: 0.8565 (t70) REVERT: A 731 ASN cc_start: 0.8558 (m110) cc_final: 0.8198 (m110) REVERT: B 27 TYR cc_start: 0.8903 (m-10) cc_final: 0.8498 (m-10) REVERT: B 32 PHE cc_start: 0.8407 (t80) cc_final: 0.8178 (t80) REVERT: B 33 GLN cc_start: 0.8422 (pp30) cc_final: 0.8161 (pp30) REVERT: B 37 GLU cc_start: 0.8246 (pp20) cc_final: 0.7810 (pp20) REVERT: B 38 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7809 (ttt90) REVERT: B 39 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8164 (mtt-85) REVERT: B 100 LEU cc_start: 0.7914 (tp) cc_final: 0.7646 (tp) REVERT: B 105 TYR cc_start: 0.7387 (m-80) cc_final: 0.7114 (m-80) REVERT: B 122 PHE cc_start: 0.8277 (m-80) cc_final: 0.7745 (m-80) REVERT: B 124 ILE cc_start: 0.8795 (mm) cc_final: 0.8399 (pt) REVERT: B 125 LEU cc_start: 0.8823 (mt) cc_final: 0.8544 (mt) REVERT: B 137 SER cc_start: 0.7935 (t) cc_final: 0.7614 (t) REVERT: B 147 MET cc_start: 0.9104 (mtt) cc_final: 0.8729 (mmp) REVERT: B 186 VAL cc_start: 0.8975 (p) cc_final: 0.8680 (m) REVERT: B 199 ILE cc_start: 0.8488 (tp) cc_final: 0.8216 (tp) REVERT: B 213 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7194 (mtp180) REVERT: B 230 GLN cc_start: 0.8483 (pp30) cc_final: 0.7960 (pp30) REVERT: B 237 LYS cc_start: 0.8964 (pttt) cc_final: 0.8245 (pttp) REVERT: B 238 ILE cc_start: 0.8694 (tp) cc_final: 0.8265 (pt) REVERT: B 241 ASN cc_start: 0.8247 (m110) cc_final: 0.7586 (m-40) REVERT: B 247 TYR cc_start: 0.8197 (m-10) cc_final: 0.7847 (m-10) REVERT: B 250 ILE cc_start: 0.8716 (pt) cc_final: 0.8510 (tp) REVERT: B 251 LEU cc_start: 0.8587 (mm) cc_final: 0.6730 (mm) REVERT: B 255 TYR cc_start: 0.7642 (m-10) cc_final: 0.7058 (m-80) REVERT: B 259 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 289 ASN cc_start: 0.9018 (m110) cc_final: 0.8758 (t0) REVERT: B 293 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8521 (mmtp) REVERT: B 303 GLU cc_start: 0.8983 (mp0) cc_final: 0.8579 (mp0) REVERT: B 318 ASN cc_start: 0.8386 (t0) cc_final: 0.7930 (t0) REVERT: B 321 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8347 (mtmt) REVERT: B 349 MET cc_start: 0.6522 (tmm) cc_final: 0.6298 (ppp) REVERT: B 383 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8123 (mm-40) REVERT: B 440 ARG cc_start: 0.7552 (mmm160) cc_final: 0.6796 (mmm160) REVERT: B 455 ILE cc_start: 0.8707 (mt) cc_final: 0.8159 (mp) REVERT: B 459 LYS cc_start: 0.8661 (mmtt) cc_final: 0.7516 (mmtt) REVERT: B 463 MET cc_start: 0.7274 (mmm) cc_final: 0.6390 (mmm) REVERT: B 473 LYS cc_start: 0.8315 (mttp) cc_final: 0.7534 (mttp) REVERT: B 477 THR cc_start: 0.8087 (m) cc_final: 0.7746 (p) REVERT: B 484 PHE cc_start: 0.8461 (t80) cc_final: 0.7831 (t80) REVERT: B 488 MET cc_start: 0.7748 (tpp) cc_final: 0.6426 (tpp) REVERT: B 491 ILE cc_start: 0.8984 (mt) cc_final: 0.8571 (mm) REVERT: B 492 LEU cc_start: 0.8775 (mt) cc_final: 0.7239 (mt) REVERT: B 496 LEU cc_start: 0.7954 (mt) cc_final: 0.7642 (mm) REVERT: B 512 ARG cc_start: 0.8592 (mtm180) cc_final: 0.8263 (mtm-85) REVERT: B 514 GLN cc_start: 0.8816 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 529 ILE cc_start: 0.8742 (mm) cc_final: 0.8434 (mp) REVERT: B 537 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7877 (mtmt) REVERT: B 563 LYS cc_start: 0.8979 (tppt) cc_final: 0.8104 (tppt) REVERT: B 577 VAL cc_start: 0.8994 (m) cc_final: 0.8699 (p) REVERT: B 578 TYR cc_start: 0.8290 (t80) cc_final: 0.7478 (t80) REVERT: B 582 LEU cc_start: 0.9035 (mt) cc_final: 0.8678 (mm) REVERT: B 656 HIS cc_start: 0.7451 (m90) cc_final: 0.7176 (m90) REVERT: B 673 VAL cc_start: 0.9236 (t) cc_final: 0.9035 (m) REVERT: B 674 ARG cc_start: 0.8874 (ttm110) cc_final: 0.8353 (ttm110) REVERT: B 677 ARG cc_start: 0.8557 (ttt180) cc_final: 0.7900 (ttm-80) REVERT: B 678 MET cc_start: 0.8164 (mmm) cc_final: 0.7818 (mmm) REVERT: B 682 GLU cc_start: 0.8229 (tp30) cc_final: 0.7523 (tp30) REVERT: B 684 GLN cc_start: 0.9122 (tp40) cc_final: 0.8795 (tp40) REVERT: B 691 TYR cc_start: 0.7604 (m-80) cc_final: 0.6919 (m-80) REVERT: B 716 ASP cc_start: 0.8213 (p0) cc_final: 0.7985 (p0) REVERT: B 720 LEU cc_start: 0.9173 (mp) cc_final: 0.8865 (mt) REVERT: B 727 LEU cc_start: 0.8987 (mt) cc_final: 0.8676 (mt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1240 time to fit residues: 60.2920 Evaluate side-chains 349 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 93 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 375 HIS B 464 GLN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.113093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090955 restraints weight = 26323.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094259 restraints weight = 15962.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096628 restraints weight = 10902.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098273 restraints weight = 8053.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099504 restraints weight = 6368.085| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10395 Z= 0.141 Angle : 0.646 9.340 14128 Z= 0.327 Chirality : 0.044 0.320 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.149 22.251 1415 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1319 helix: 0.56 (0.18), residues: 832 sheet: -1.05 (1.07), residues: 33 loop : -2.54 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 586 TYR 0.015 0.001 TYR B 377 PHE 0.026 0.001 PHE A 115 TRP 0.020 0.002 TRP B 74 HIS 0.003 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00303 (10395) covalent geometry : angle 0.64587 (14128) hydrogen bonds : bond 0.03776 ( 546) hydrogen bonds : angle 3.88071 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.400 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 20 TYR cc_start: 0.8432 (t80) cc_final: 0.8101 (t80) REVERT: A 38 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7604 (ttm110) REVERT: A 96 LEU cc_start: 0.8814 (mt) cc_final: 0.8474 (mm) REVERT: A 105 TYR cc_start: 0.8396 (m-80) cc_final: 0.8103 (m-80) REVERT: A 119 SER cc_start: 0.8740 (t) cc_final: 0.8264 (p) REVERT: A 121 PHE cc_start: 0.7662 (t80) cc_final: 0.7326 (t80) REVERT: A 161 PHE cc_start: 0.7921 (m-10) cc_final: 0.6525 (m-10) REVERT: A 194 LEU cc_start: 0.8410 (tp) cc_final: 0.8089 (mm) REVERT: A 211 ILE cc_start: 0.9030 (tt) cc_final: 0.8751 (tp) REVERT: A 230 GLN cc_start: 0.8868 (mt0) cc_final: 0.8109 (tm-30) REVERT: A 234 SER cc_start: 0.9179 (m) cc_final: 0.8589 (p) REVERT: A 235 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8261 (mm-40) REVERT: A 237 LYS cc_start: 0.8967 (pttp) cc_final: 0.8442 (pttm) REVERT: A 240 LEU cc_start: 0.8567 (mm) cc_final: 0.8336 (mp) REVERT: A 252 SER cc_start: 0.8278 (p) cc_final: 0.7803 (m) REVERT: A 272 PHE cc_start: 0.8127 (t80) cc_final: 0.7784 (t80) REVERT: A 276 LEU cc_start: 0.8744 (pp) cc_final: 0.8494 (pp) REVERT: A 279 ILE cc_start: 0.9106 (mm) cc_final: 0.8740 (tp) REVERT: A 281 VAL cc_start: 0.8887 (m) cc_final: 0.8670 (p) REVERT: A 282 CYS cc_start: 0.8589 (p) cc_final: 0.8040 (p) REVERT: A 283 MET cc_start: 0.7926 (mmp) cc_final: 0.7263 (mmp) REVERT: A 285 VAL cc_start: 0.8753 (m) cc_final: 0.8289 (p) REVERT: A 286 LYS cc_start: 0.8880 (tppt) cc_final: 0.8647 (tppt) REVERT: A 289 ASN cc_start: 0.8925 (m110) cc_final: 0.8305 (m110) REVERT: A 293 LYS cc_start: 0.8280 (tppt) cc_final: 0.7826 (tppt) REVERT: A 305 ILE cc_start: 0.8681 (tp) cc_final: 0.8467 (tp) REVERT: A 309 ILE cc_start: 0.8924 (tp) cc_final: 0.8626 (pt) REVERT: A 321 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8248 (ttpp) REVERT: A 329 LYS cc_start: 0.6413 (pttt) cc_final: 0.6095 (ttpp) REVERT: A 345 LEU cc_start: 0.8404 (mt) cc_final: 0.7526 (mt) REVERT: A 349 MET cc_start: 0.7110 (mtm) cc_final: 0.6604 (mtm) REVERT: A 353 SER cc_start: 0.9007 (m) cc_final: 0.8674 (p) REVERT: A 369 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8203 (mmtt) REVERT: A 371 TYR cc_start: 0.8291 (m-80) cc_final: 0.7702 (m-80) REVERT: A 382 ASN cc_start: 0.8845 (m110) cc_final: 0.8616 (t0) REVERT: A 384 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 385 PHE cc_start: 0.8129 (t80) cc_final: 0.7417 (t80) REVERT: A 392 ASN cc_start: 0.9237 (m-40) cc_final: 0.8884 (m-40) REVERT: A 394 PHE cc_start: 0.8316 (t80) cc_final: 0.7746 (t80) REVERT: A 397 PHE cc_start: 0.7865 (t80) cc_final: 0.7619 (t80) REVERT: A 414 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 432 MET cc_start: 0.8286 (tpt) cc_final: 0.7896 (tpt) REVERT: A 443 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 454 VAL cc_start: 0.9038 (t) cc_final: 0.8838 (t) REVERT: A 458 LEU cc_start: 0.8604 (mt) cc_final: 0.8342 (mt) REVERT: A 459 LYS cc_start: 0.8459 (tppp) cc_final: 0.6628 (tppp) REVERT: A 461 MET cc_start: 0.9044 (mtp) cc_final: 0.8757 (mtp) REVERT: A 463 MET cc_start: 0.8085 (mmp) cc_final: 0.6854 (mmp) REVERT: A 467 ASP cc_start: 0.7922 (p0) cc_final: 0.7654 (p0) REVERT: A 470 ARG cc_start: 0.7979 (ptp-170) cc_final: 0.7701 (ptt-90) REVERT: A 473 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8284 (mtpt) REVERT: A 476 LYS cc_start: 0.8664 (mttm) cc_final: 0.8417 (mmtt) REVERT: A 496 LEU cc_start: 0.8824 (mm) cc_final: 0.8518 (tp) REVERT: A 514 GLN cc_start: 0.8287 (tt0) cc_final: 0.7744 (tm-30) REVERT: A 530 TYR cc_start: 0.8230 (m-10) cc_final: 0.7874 (m-10) REVERT: A 536 TYR cc_start: 0.8338 (m-80) cc_final: 0.7780 (m-80) REVERT: A 537 LYS cc_start: 0.8465 (tttt) cc_final: 0.8130 (tttt) REVERT: A 549 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7090 (tpp-160) REVERT: A 560 ASP cc_start: 0.8351 (m-30) cc_final: 0.8127 (t0) REVERT: A 563 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8111 (mmmt) REVERT: A 564 LYS cc_start: 0.8895 (tppt) cc_final: 0.8385 (tppt) REVERT: A 677 ARG cc_start: 0.8505 (ptm160) cc_final: 0.8261 (ptm160) REVERT: A 678 MET cc_start: 0.8193 (mmm) cc_final: 0.7795 (mmm) REVERT: A 682 GLU cc_start: 0.8333 (pp20) cc_final: 0.8112 (tm-30) REVERT: A 687 ASP cc_start: 0.8397 (t0) cc_final: 0.8107 (p0) REVERT: A 697 ASP cc_start: 0.8563 (m-30) cc_final: 0.7684 (p0) REVERT: A 701 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 705 GLN cc_start: 0.7932 (tp40) cc_final: 0.7594 (tm-30) REVERT: A 723 HIS cc_start: 0.8057 (t70) cc_final: 0.7820 (t70) REVERT: A 724 ASP cc_start: 0.8417 (m-30) cc_final: 0.7887 (m-30) REVERT: A 727 LEU cc_start: 0.8824 (mm) cc_final: 0.8201 (mt) REVERT: A 728 HIS cc_start: 0.8831 (t70) cc_final: 0.8584 (t70) REVERT: A 731 ASN cc_start: 0.8549 (m110) cc_final: 0.8201 (m110) REVERT: B 27 TYR cc_start: 0.8866 (m-10) cc_final: 0.8231 (m-10) REVERT: B 30 LEU cc_start: 0.8385 (pt) cc_final: 0.8176 (pt) REVERT: B 32 PHE cc_start: 0.8419 (t80) cc_final: 0.8204 (t80) REVERT: B 33 GLN cc_start: 0.8417 (pp30) cc_final: 0.8128 (pp30) REVERT: B 37 GLU cc_start: 0.8246 (pp20) cc_final: 0.7979 (pp20) REVERT: B 38 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7810 (ttt90) REVERT: B 39 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8026 (mtt-85) REVERT: B 105 TYR cc_start: 0.7329 (m-80) cc_final: 0.6997 (m-80) REVERT: B 122 PHE cc_start: 0.8282 (m-80) cc_final: 0.7710 (m-80) REVERT: B 124 ILE cc_start: 0.8818 (mm) cc_final: 0.8402 (pt) REVERT: B 125 LEU cc_start: 0.8815 (mt) cc_final: 0.8516 (mt) REVERT: B 137 SER cc_start: 0.7988 (t) cc_final: 0.7644 (t) REVERT: B 147 MET cc_start: 0.9069 (mtt) cc_final: 0.8751 (mmp) REVERT: B 186 VAL cc_start: 0.8972 (p) cc_final: 0.8666 (m) REVERT: B 199 ILE cc_start: 0.8405 (tp) cc_final: 0.7786 (pt) REVERT: B 207 GLN cc_start: 0.9029 (tt0) cc_final: 0.8284 (tm-30) REVERT: B 212 VAL cc_start: 0.8564 (m) cc_final: 0.8318 (t) REVERT: B 230 GLN cc_start: 0.8501 (pp30) cc_final: 0.7955 (pp30) REVERT: B 235 GLN cc_start: 0.8338 (pp30) cc_final: 0.7968 (pp30) REVERT: B 236 LEU cc_start: 0.8702 (tp) cc_final: 0.8123 (mt) REVERT: B 237 LYS cc_start: 0.8934 (pttt) cc_final: 0.8413 (pttp) REVERT: B 238 ILE cc_start: 0.8686 (tp) cc_final: 0.8260 (pt) REVERT: B 241 ASN cc_start: 0.8103 (m110) cc_final: 0.7592 (m-40) REVERT: B 247 TYR cc_start: 0.8154 (m-10) cc_final: 0.7839 (m-10) REVERT: B 250 ILE cc_start: 0.8710 (pt) cc_final: 0.8363 (mm) REVERT: B 251 LEU cc_start: 0.8548 (mm) cc_final: 0.6713 (mm) REVERT: B 255 TYR cc_start: 0.7719 (m-10) cc_final: 0.7081 (m-80) REVERT: B 257 LEU cc_start: 0.8662 (tp) cc_final: 0.8172 (tp) REVERT: B 259 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 260 ILE cc_start: 0.9070 (mt) cc_final: 0.8673 (mt) REVERT: B 261 PHE cc_start: 0.8131 (m-80) cc_final: 0.7441 (m-80) REVERT: B 289 ASN cc_start: 0.9003 (m-40) cc_final: 0.8774 (m110) REVERT: B 303 GLU cc_start: 0.9025 (mp0) cc_final: 0.8603 (mp0) REVERT: B 383 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8209 (mm-40) REVERT: B 440 ARG cc_start: 0.7502 (mmm160) cc_final: 0.6743 (mmm160) REVERT: B 447 LYS cc_start: 0.8957 (mttt) cc_final: 0.8692 (ptpp) REVERT: B 455 ILE cc_start: 0.8649 (mt) cc_final: 0.8059 (mm) REVERT: B 459 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7568 (mmtt) REVERT: B 463 MET cc_start: 0.7291 (mmm) cc_final: 0.6358 (mmm) REVERT: B 473 LYS cc_start: 0.8323 (mttp) cc_final: 0.7538 (mttp) REVERT: B 476 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8181 (mtpp) REVERT: B 477 THR cc_start: 0.8067 (m) cc_final: 0.7725 (p) REVERT: B 482 TRP cc_start: 0.8416 (t60) cc_final: 0.8046 (t60) REVERT: B 484 PHE cc_start: 0.8383 (t80) cc_final: 0.7784 (t80) REVERT: B 488 MET cc_start: 0.7747 (tpp) cc_final: 0.6537 (tpp) REVERT: B 491 ILE cc_start: 0.8998 (mt) cc_final: 0.8723 (mm) REVERT: B 492 LEU cc_start: 0.8749 (mt) cc_final: 0.7379 (mt) REVERT: B 496 LEU cc_start: 0.7914 (mt) cc_final: 0.7573 (mm) REVERT: B 512 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8225 (mtm-85) REVERT: B 514 GLN cc_start: 0.8807 (tt0) cc_final: 0.8364 (tm-30) REVERT: B 529 ILE cc_start: 0.8645 (mm) cc_final: 0.8324 (mp) REVERT: B 537 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7782 (mtmm) REVERT: B 549 ARG cc_start: 0.8256 (ptm160) cc_final: 0.8010 (ptm-80) REVERT: B 563 LYS cc_start: 0.8962 (tppt) cc_final: 0.8098 (tppt) REVERT: B 577 VAL cc_start: 0.8961 (m) cc_final: 0.8675 (p) REVERT: B 578 TYR cc_start: 0.8269 (t80) cc_final: 0.7445 (t80) REVERT: B 580 LYS cc_start: 0.8906 (tmtt) cc_final: 0.8447 (tttt) REVERT: B 582 LEU cc_start: 0.9018 (mt) cc_final: 0.8670 (mm) REVERT: B 656 HIS cc_start: 0.7473 (m90) cc_final: 0.7189 (m90) REVERT: B 674 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8341 (ttm110) REVERT: B 677 ARG cc_start: 0.8560 (ttt180) cc_final: 0.7912 (ttm-80) REVERT: B 678 MET cc_start: 0.8176 (mmm) cc_final: 0.7816 (mmm) REVERT: B 682 GLU cc_start: 0.8242 (tp30) cc_final: 0.7532 (tp30) REVERT: B 691 TYR cc_start: 0.7541 (m-80) cc_final: 0.6830 (m-80) REVERT: B 716 ASP cc_start: 0.8203 (p0) cc_final: 0.7494 (t0) REVERT: B 720 LEU cc_start: 0.9185 (mp) cc_final: 0.8869 (mt) REVERT: B 727 LEU cc_start: 0.8926 (mt) cc_final: 0.8449 (mt) REVERT: B 730 GLN cc_start: 0.8958 (tt0) cc_final: 0.8340 (tm-30) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1201 time to fit residues: 57.5752 Evaluate side-chains 328 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090355 restraints weight = 26307.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093685 restraints weight = 15816.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096021 restraints weight = 10739.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097710 restraints weight = 7897.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098930 restraints weight = 6209.372| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10395 Z= 0.159 Angle : 0.657 9.590 14128 Z= 0.337 Chirality : 0.044 0.334 1716 Planarity : 0.004 0.055 1757 Dihedral : 4.214 22.062 1415 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1319 helix: 0.60 (0.18), residues: 819 sheet: -1.30 (1.02), residues: 33 loop : -2.34 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 213 TYR 0.018 0.001 TYR A 361 PHE 0.023 0.001 PHE B 261 TRP 0.021 0.002 TRP B 74 HIS 0.003 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00336 (10395) covalent geometry : angle 0.65730 (14128) hydrogen bonds : bond 0.03839 ( 546) hydrogen bonds : angle 3.93172 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.361 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: A 20 TYR cc_start: 0.8421 (t80) cc_final: 0.8112 (t80) REVERT: A 38 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7565 (ttm110) REVERT: A 96 LEU cc_start: 0.8830 (mt) cc_final: 0.8495 (mm) REVERT: A 105 TYR cc_start: 0.8472 (m-80) cc_final: 0.8113 (m-80) REVERT: A 119 SER cc_start: 0.8703 (t) cc_final: 0.8279 (p) REVERT: A 121 PHE cc_start: 0.7652 (t80) cc_final: 0.7331 (t80) REVERT: A 161 PHE cc_start: 0.7930 (m-10) cc_final: 0.6512 (m-10) REVERT: A 194 LEU cc_start: 0.8402 (tp) cc_final: 0.8192 (tp) REVERT: A 211 ILE cc_start: 0.9041 (tt) cc_final: 0.8748 (tp) REVERT: A 230 GLN cc_start: 0.8867 (mt0) cc_final: 0.8096 (tm-30) REVERT: A 235 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8306 (mm-40) REVERT: A 237 LYS cc_start: 0.8986 (pttp) cc_final: 0.8428 (pttm) REVERT: A 252 SER cc_start: 0.8321 (p) cc_final: 0.7838 (m) REVERT: A 272 PHE cc_start: 0.8121 (t80) cc_final: 0.7810 (t80) REVERT: A 276 LEU cc_start: 0.8744 (pp) cc_final: 0.8491 (pp) REVERT: A 279 ILE cc_start: 0.9090 (mm) cc_final: 0.8709 (tp) REVERT: A 281 VAL cc_start: 0.8891 (m) cc_final: 0.8681 (p) REVERT: A 282 CYS cc_start: 0.8555 (p) cc_final: 0.8012 (p) REVERT: A 283 MET cc_start: 0.7888 (mmp) cc_final: 0.7201 (mmp) REVERT: A 285 VAL cc_start: 0.8750 (m) cc_final: 0.8296 (p) REVERT: A 286 LYS cc_start: 0.8874 (tppt) cc_final: 0.8638 (tppt) REVERT: A 289 ASN cc_start: 0.8907 (m110) cc_final: 0.8222 (m110) REVERT: A 293 LYS cc_start: 0.8250 (tppt) cc_final: 0.7787 (tppt) REVERT: A 305 ILE cc_start: 0.8709 (tp) cc_final: 0.8459 (tp) REVERT: A 309 ILE cc_start: 0.8944 (tp) cc_final: 0.8651 (pt) REVERT: A 321 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8131 (ttpp) REVERT: A 329 LYS cc_start: 0.6330 (pttt) cc_final: 0.5971 (ttpp) REVERT: A 345 LEU cc_start: 0.8438 (mt) cc_final: 0.7532 (mt) REVERT: A 346 PHE cc_start: 0.8043 (m-10) cc_final: 0.7762 (m-10) REVERT: A 349 MET cc_start: 0.7076 (mtm) cc_final: 0.6564 (mtm) REVERT: A 353 SER cc_start: 0.9018 (m) cc_final: 0.8721 (p) REVERT: A 369 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8292 (mmtt) REVERT: A 371 TYR cc_start: 0.8310 (m-80) cc_final: 0.7692 (m-80) REVERT: A 382 ASN cc_start: 0.8848 (m110) cc_final: 0.8614 (t0) REVERT: A 384 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 385 PHE cc_start: 0.8057 (t80) cc_final: 0.7299 (t80) REVERT: A 392 ASN cc_start: 0.9241 (m-40) cc_final: 0.8901 (m-40) REVERT: A 394 PHE cc_start: 0.8336 (t80) cc_final: 0.7747 (t80) REVERT: A 414 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 432 MET cc_start: 0.8328 (tpt) cc_final: 0.7910 (tpt) REVERT: A 443 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 454 VAL cc_start: 0.9025 (t) cc_final: 0.8814 (t) REVERT: A 458 LEU cc_start: 0.8709 (mt) cc_final: 0.8478 (mt) REVERT: A 459 LYS cc_start: 0.8470 (tppp) cc_final: 0.6741 (tppp) REVERT: A 463 MET cc_start: 0.8042 (mmp) cc_final: 0.7085 (mmp) REVERT: A 467 ASP cc_start: 0.7896 (p0) cc_final: 0.7607 (p0) REVERT: A 470 ARG cc_start: 0.7978 (ptp-170) cc_final: 0.7705 (ptt-90) REVERT: A 472 TRP cc_start: 0.8572 (t-100) cc_final: 0.8282 (t-100) REVERT: A 473 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8285 (mtpt) REVERT: A 476 LYS cc_start: 0.8704 (mttm) cc_final: 0.8160 (mmmm) REVERT: A 496 LEU cc_start: 0.8844 (mm) cc_final: 0.8533 (tp) REVERT: A 537 LYS cc_start: 0.8460 (tttt) cc_final: 0.8109 (tttt) REVERT: A 549 ARG cc_start: 0.7940 (ttt90) cc_final: 0.7239 (tpp-160) REVERT: A 560 ASP cc_start: 0.8374 (m-30) cc_final: 0.8169 (t0) REVERT: A 563 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8203 (mmmt) REVERT: A 564 LYS cc_start: 0.8948 (tppt) cc_final: 0.8397 (tppt) REVERT: A 677 ARG cc_start: 0.8499 (ptm160) cc_final: 0.8233 (ptm160) REVERT: A 678 MET cc_start: 0.8108 (mmm) cc_final: 0.7739 (mmm) REVERT: A 682 GLU cc_start: 0.8391 (pp20) cc_final: 0.8056 (tm-30) REVERT: A 687 ASP cc_start: 0.8402 (t0) cc_final: 0.7978 (t0) REVERT: A 697 ASP cc_start: 0.8587 (m-30) cc_final: 0.8195 (p0) REVERT: A 701 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7730 (mm-30) REVERT: A 705 GLN cc_start: 0.7902 (tp40) cc_final: 0.7507 (tm-30) REVERT: A 723 HIS cc_start: 0.8035 (t70) cc_final: 0.7689 (t70) REVERT: A 724 ASP cc_start: 0.8354 (m-30) cc_final: 0.7782 (m-30) REVERT: A 727 LEU cc_start: 0.8830 (mm) cc_final: 0.8218 (mt) REVERT: A 728 HIS cc_start: 0.8836 (t70) cc_final: 0.8593 (t70) REVERT: A 731 ASN cc_start: 0.8466 (m110) cc_final: 0.8074 (m110) REVERT: B 27 TYR cc_start: 0.8902 (m-10) cc_final: 0.8297 (m-10) REVERT: B 32 PHE cc_start: 0.8417 (t80) cc_final: 0.8190 (t80) REVERT: B 33 GLN cc_start: 0.8376 (pp30) cc_final: 0.8048 (pp30) REVERT: B 105 TYR cc_start: 0.7272 (m-80) cc_final: 0.6982 (m-80) REVERT: B 122 PHE cc_start: 0.8299 (m-80) cc_final: 0.7727 (m-80) REVERT: B 124 ILE cc_start: 0.8837 (mm) cc_final: 0.8431 (pt) REVERT: B 125 LEU cc_start: 0.8822 (mt) cc_final: 0.8519 (mt) REVERT: B 137 SER cc_start: 0.7978 (t) cc_final: 0.7632 (t) REVERT: B 147 MET cc_start: 0.9067 (mtt) cc_final: 0.8754 (mmp) REVERT: B 186 VAL cc_start: 0.8953 (p) cc_final: 0.8634 (m) REVERT: B 199 ILE cc_start: 0.8301 (tp) cc_final: 0.7936 (pt) REVERT: B 207 GLN cc_start: 0.9035 (tt0) cc_final: 0.8284 (tm-30) REVERT: B 212 VAL cc_start: 0.8672 (m) cc_final: 0.8446 (t) REVERT: B 230 GLN cc_start: 0.8495 (pp30) cc_final: 0.7929 (pp30) REVERT: B 237 LYS cc_start: 0.8928 (pttt) cc_final: 0.8423 (pttp) REVERT: B 238 ILE cc_start: 0.8702 (tp) cc_final: 0.8267 (pt) REVERT: B 241 ASN cc_start: 0.8166 (m110) cc_final: 0.7676 (m-40) REVERT: B 247 TYR cc_start: 0.8246 (m-10) cc_final: 0.7874 (m-10) REVERT: B 250 ILE cc_start: 0.8747 (pt) cc_final: 0.8388 (mm) REVERT: B 251 LEU cc_start: 0.8569 (mm) cc_final: 0.6707 (mm) REVERT: B 255 TYR cc_start: 0.7710 (m-10) cc_final: 0.7111 (m-80) REVERT: B 257 LEU cc_start: 0.8658 (tp) cc_final: 0.8106 (tp) REVERT: B 259 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 260 ILE cc_start: 0.9064 (mt) cc_final: 0.8634 (mt) REVERT: B 261 PHE cc_start: 0.8120 (m-80) cc_final: 0.7343 (m-80) REVERT: B 286 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8665 (ptpp) REVERT: B 303 GLU cc_start: 0.9029 (mp0) cc_final: 0.8590 (mp0) REVERT: B 383 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8209 (mm-40) REVERT: B 447 LYS cc_start: 0.8902 (mttt) cc_final: 0.8627 (mttt) REVERT: B 455 ILE cc_start: 0.8808 (mt) cc_final: 0.8426 (mp) REVERT: B 459 LYS cc_start: 0.8700 (mmtt) cc_final: 0.7545 (mmtt) REVERT: B 461 MET cc_start: 0.8685 (mtp) cc_final: 0.8451 (mtp) REVERT: B 463 MET cc_start: 0.7285 (mmm) cc_final: 0.6327 (mmm) REVERT: B 471 LEU cc_start: 0.8272 (mm) cc_final: 0.8010 (mm) REVERT: B 473 LYS cc_start: 0.8350 (mttp) cc_final: 0.7519 (pttt) REVERT: B 476 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8192 (mtpp) REVERT: B 477 THR cc_start: 0.8053 (m) cc_final: 0.7695 (p) REVERT: B 482 TRP cc_start: 0.8439 (t60) cc_final: 0.8054 (t60) REVERT: B 484 PHE cc_start: 0.8373 (t80) cc_final: 0.7776 (t80) REVERT: B 488 MET cc_start: 0.7694 (tpp) cc_final: 0.6524 (tpp) REVERT: B 491 ILE cc_start: 0.9009 (mt) cc_final: 0.8738 (mm) REVERT: B 492 LEU cc_start: 0.8757 (mt) cc_final: 0.7372 (mt) REVERT: B 496 LEU cc_start: 0.7917 (mt) cc_final: 0.7588 (mm) REVERT: B 512 ARG cc_start: 0.8553 (mtm180) cc_final: 0.8148 (mtm-85) REVERT: B 514 GLN cc_start: 0.8794 (tt0) cc_final: 0.8342 (tm-30) REVERT: B 529 ILE cc_start: 0.8688 (mm) cc_final: 0.8415 (mp) REVERT: B 537 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7797 (mtmm) REVERT: B 549 ARG cc_start: 0.8307 (ptm160) cc_final: 0.8055 (ptm-80) REVERT: B 563 LYS cc_start: 0.8967 (tppt) cc_final: 0.8119 (tppt) REVERT: B 577 VAL cc_start: 0.8976 (m) cc_final: 0.8705 (p) REVERT: B 578 TYR cc_start: 0.8246 (t80) cc_final: 0.7467 (t80) REVERT: B 580 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8348 (ttmt) REVERT: B 582 LEU cc_start: 0.9006 (mt) cc_final: 0.8669 (mm) REVERT: B 586 ARG cc_start: 0.8287 (ppt170) cc_final: 0.7871 (ttp80) REVERT: B 656 HIS cc_start: 0.7478 (m90) cc_final: 0.7209 (m90) REVERT: B 674 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8388 (ttm110) REVERT: B 677 ARG cc_start: 0.8528 (ttt180) cc_final: 0.7900 (ttm-80) REVERT: B 678 MET cc_start: 0.8149 (mmm) cc_final: 0.7835 (mmm) REVERT: B 682 GLU cc_start: 0.8250 (tp30) cc_final: 0.7541 (tp30) REVERT: B 691 TYR cc_start: 0.7581 (m-80) cc_final: 0.6898 (m-80) REVERT: B 716 ASP cc_start: 0.8232 (p0) cc_final: 0.7629 (t0) REVERT: B 720 LEU cc_start: 0.9194 (mp) cc_final: 0.8888 (mt) REVERT: B 727 LEU cc_start: 0.8951 (mt) cc_final: 0.7538 (mt) REVERT: B 730 GLN cc_start: 0.8885 (tt0) cc_final: 0.8432 (pp30) REVERT: B 731 ASN cc_start: 0.8540 (p0) cc_final: 0.7536 (p0) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1141 time to fit residues: 54.4408 Evaluate side-chains 326 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 96 optimal weight: 0.0670 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS B 464 GLN B 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.114382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092409 restraints weight = 26056.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095728 restraints weight = 15759.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098151 restraints weight = 10802.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099836 restraints weight = 7901.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101131 restraints weight = 6219.902| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10395 Z= 0.130 Angle : 0.654 9.741 14128 Z= 0.330 Chirality : 0.044 0.336 1716 Planarity : 0.004 0.053 1757 Dihedral : 4.229 23.372 1415 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1319 helix: 0.57 (0.18), residues: 829 sheet: -1.19 (1.00), residues: 35 loop : -2.44 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 38 TYR 0.018 0.001 TYR B 377 PHE 0.031 0.001 PHE B 203 TRP 0.029 0.002 TRP A 472 HIS 0.006 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00287 (10395) covalent geometry : angle 0.65398 (14128) hydrogen bonds : bond 0.03753 ( 546) hydrogen bonds : angle 3.87568 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.300 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 20 TYR cc_start: 0.8364 (t80) cc_final: 0.8069 (t80) REVERT: A 29 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 38 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7530 (ttm110) REVERT: A 66 LYS cc_start: 0.8882 (tppt) cc_final: 0.8680 (tppt) REVERT: A 96 LEU cc_start: 0.8824 (mt) cc_final: 0.8478 (mm) REVERT: A 103 MET cc_start: 0.8017 (mpp) cc_final: 0.7785 (mpp) REVERT: A 105 TYR cc_start: 0.8200 (m-80) cc_final: 0.7950 (m-80) REVERT: A 119 SER cc_start: 0.8663 (t) cc_final: 0.8296 (p) REVERT: A 121 PHE cc_start: 0.7550 (t80) cc_final: 0.7264 (t80) REVERT: A 161 PHE cc_start: 0.7858 (m-10) cc_final: 0.5891 (m-10) REVERT: A 181 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.7082 (tpp-160) REVERT: A 185 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8357 (mtm-85) REVERT: A 194 LEU cc_start: 0.8331 (tp) cc_final: 0.8028 (mm) REVERT: A 200 GLN cc_start: 0.8757 (mt0) cc_final: 0.7601 (tt0) REVERT: A 211 ILE cc_start: 0.9006 (tt) cc_final: 0.8726 (tp) REVERT: A 213 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6983 (mtt-85) REVERT: A 230 GLN cc_start: 0.8895 (mt0) cc_final: 0.8204 (tp40) REVERT: A 237 LYS cc_start: 0.8955 (pttp) cc_final: 0.8394 (pttm) REVERT: A 252 SER cc_start: 0.8246 (p) cc_final: 0.7748 (m) REVERT: A 272 PHE cc_start: 0.8055 (t80) cc_final: 0.7664 (t80) REVERT: A 276 LEU cc_start: 0.8712 (pp) cc_final: 0.8448 (pp) REVERT: A 279 ILE cc_start: 0.9056 (mm) cc_final: 0.8715 (tp) REVERT: A 282 CYS cc_start: 0.8543 (p) cc_final: 0.8005 (p) REVERT: A 283 MET cc_start: 0.7891 (mmp) cc_final: 0.7189 (mmp) REVERT: A 285 VAL cc_start: 0.8690 (m) cc_final: 0.8255 (p) REVERT: A 286 LYS cc_start: 0.8848 (tppt) cc_final: 0.8610 (tppt) REVERT: A 289 ASN cc_start: 0.8933 (m110) cc_final: 0.8371 (m110) REVERT: A 293 LYS cc_start: 0.8216 (tppt) cc_final: 0.7754 (tppt) REVERT: A 305 ILE cc_start: 0.8661 (tp) cc_final: 0.8418 (tp) REVERT: A 309 ILE cc_start: 0.8913 (tp) cc_final: 0.8615 (pt) REVERT: A 321 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8082 (ttpp) REVERT: A 329 LYS cc_start: 0.6248 (pttt) cc_final: 0.5869 (ttpp) REVERT: A 345 LEU cc_start: 0.8403 (mt) cc_final: 0.7501 (mt) REVERT: A 349 MET cc_start: 0.7053 (mtm) cc_final: 0.6573 (mtm) REVERT: A 353 SER cc_start: 0.8970 (m) cc_final: 0.8555 (p) REVERT: A 369 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8275 (mmtt) REVERT: A 371 TYR cc_start: 0.8330 (m-80) cc_final: 0.7730 (m-80) REVERT: A 383 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8128 (mm110) REVERT: A 384 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 392 ASN cc_start: 0.9236 (m-40) cc_final: 0.8922 (m-40) REVERT: A 394 PHE cc_start: 0.8256 (t80) cc_final: 0.7722 (t80) REVERT: A 397 PHE cc_start: 0.7864 (t80) cc_final: 0.7292 (t80) REVERT: A 414 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 432 MET cc_start: 0.8261 (tpt) cc_final: 0.7762 (tpt) REVERT: A 443 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 454 VAL cc_start: 0.9033 (t) cc_final: 0.8811 (t) REVERT: A 458 LEU cc_start: 0.8624 (mt) cc_final: 0.8292 (mt) REVERT: A 459 LYS cc_start: 0.8476 (tppp) cc_final: 0.6674 (tppp) REVERT: A 461 MET cc_start: 0.8880 (mtm) cc_final: 0.8577 (ttp) REVERT: A 463 MET cc_start: 0.8099 (mmp) cc_final: 0.7137 (mmp) REVERT: A 467 ASP cc_start: 0.7945 (p0) cc_final: 0.7642 (p0) REVERT: A 470 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7636 (ptt-90) REVERT: A 472 TRP cc_start: 0.8510 (t-100) cc_final: 0.7908 (t-100) REVERT: A 473 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8341 (mtpt) REVERT: A 476 LYS cc_start: 0.8649 (mttm) cc_final: 0.7830 (mmmt) REVERT: A 486 CYS cc_start: 0.8796 (t) cc_final: 0.8253 (p) REVERT: A 496 LEU cc_start: 0.8630 (mm) cc_final: 0.8390 (tp) REVERT: A 514 GLN cc_start: 0.8369 (tt0) cc_final: 0.7668 (tm-30) REVERT: A 524 VAL cc_start: 0.9310 (t) cc_final: 0.8991 (t) REVERT: A 537 LYS cc_start: 0.8404 (tttt) cc_final: 0.8063 (tttt) REVERT: A 540 GLU cc_start: 0.7598 (pt0) cc_final: 0.6859 (pm20) REVERT: A 546 LYS cc_start: 0.8488 (tptm) cc_final: 0.7946 (tptm) REVERT: A 549 ARG cc_start: 0.7826 (ttt90) cc_final: 0.7004 (ttm-80) REVERT: A 560 ASP cc_start: 0.8339 (m-30) cc_final: 0.8130 (t0) REVERT: A 563 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8119 (mmmt) REVERT: A 564 LYS cc_start: 0.8939 (tppt) cc_final: 0.8493 (tppt) REVERT: A 677 ARG cc_start: 0.8502 (ptm160) cc_final: 0.7883 (ttt180) REVERT: A 678 MET cc_start: 0.8109 (mmm) cc_final: 0.7744 (mmm) REVERT: A 682 GLU cc_start: 0.8449 (pp20) cc_final: 0.8166 (tm-30) REVERT: A 687 ASP cc_start: 0.8392 (t0) cc_final: 0.7981 (t0) REVERT: A 689 ASN cc_start: 0.8019 (m-40) cc_final: 0.7811 (m-40) REVERT: A 697 ASP cc_start: 0.8577 (m-30) cc_final: 0.8246 (p0) REVERT: A 701 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7782 (mm-30) REVERT: A 705 GLN cc_start: 0.7945 (tp40) cc_final: 0.7526 (tm-30) REVERT: A 715 LYS cc_start: 0.8275 (mttm) cc_final: 0.7802 (mttm) REVERT: A 724 ASP cc_start: 0.8272 (m-30) cc_final: 0.7731 (m-30) REVERT: A 727 LEU cc_start: 0.8690 (mm) cc_final: 0.8159 (mm) REVERT: A 728 HIS cc_start: 0.8783 (t70) cc_final: 0.8428 (t-90) REVERT: A 731 ASN cc_start: 0.8495 (m110) cc_final: 0.8135 (m110) REVERT: B 27 TYR cc_start: 0.8864 (m-10) cc_final: 0.8242 (m-10) REVERT: B 29 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 32 PHE cc_start: 0.8392 (t80) cc_final: 0.8175 (t80) REVERT: B 33 GLN cc_start: 0.8356 (pp30) cc_final: 0.8038 (pp30) REVERT: B 37 GLU cc_start: 0.8105 (pp20) cc_final: 0.7827 (pp20) REVERT: B 38 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.8014 (mtp85) REVERT: B 39 ARG cc_start: 0.8297 (mtt180) cc_final: 0.8069 (mtt180) REVERT: B 105 TYR cc_start: 0.7173 (m-80) cc_final: 0.6884 (m-80) REVERT: B 122 PHE cc_start: 0.8230 (m-80) cc_final: 0.7722 (m-80) REVERT: B 124 ILE cc_start: 0.8810 (mm) cc_final: 0.8380 (pt) REVERT: B 125 LEU cc_start: 0.8787 (mt) cc_final: 0.8495 (mt) REVERT: B 137 SER cc_start: 0.8060 (t) cc_final: 0.7716 (t) REVERT: B 147 MET cc_start: 0.9086 (mtt) cc_final: 0.8660 (mtt) REVERT: B 186 VAL cc_start: 0.8950 (p) cc_final: 0.8639 (m) REVERT: B 196 VAL cc_start: 0.8994 (t) cc_final: 0.8576 (t) REVERT: B 199 ILE cc_start: 0.8371 (tp) cc_final: 0.7875 (pt) REVERT: B 203 PHE cc_start: 0.6476 (m-80) cc_final: 0.6216 (m-80) REVERT: B 207 GLN cc_start: 0.8979 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 212 VAL cc_start: 0.8648 (m) cc_final: 0.8427 (t) REVERT: B 230 GLN cc_start: 0.8496 (pp30) cc_final: 0.7897 (pp30) REVERT: B 235 GLN cc_start: 0.8352 (pp30) cc_final: 0.8109 (pp30) REVERT: B 236 LEU cc_start: 0.8774 (tp) cc_final: 0.8365 (mt) REVERT: B 237 LYS cc_start: 0.8850 (pttt) cc_final: 0.8365 (pttm) REVERT: B 238 ILE cc_start: 0.8714 (tp) cc_final: 0.8287 (pt) REVERT: B 241 ASN cc_start: 0.8041 (m110) cc_final: 0.7652 (m-40) REVERT: B 247 TYR cc_start: 0.8150 (m-10) cc_final: 0.7848 (m-10) REVERT: B 250 ILE cc_start: 0.8733 (pt) cc_final: 0.8379 (mm) REVERT: B 251 LEU cc_start: 0.8554 (mm) cc_final: 0.6690 (mm) REVERT: B 255 TYR cc_start: 0.7714 (m-10) cc_final: 0.7080 (m-80) REVERT: B 257 LEU cc_start: 0.8666 (tp) cc_final: 0.8096 (tp) REVERT: B 259 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 260 ILE cc_start: 0.9062 (mt) cc_final: 0.8666 (mt) REVERT: B 261 PHE cc_start: 0.8097 (m-80) cc_final: 0.7321 (m-80) REVERT: B 303 GLU cc_start: 0.9062 (mp0) cc_final: 0.8610 (mp0) REVERT: B 383 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8181 (mm-40) REVERT: B 447 LYS cc_start: 0.8938 (mttt) cc_final: 0.8627 (mttt) REVERT: B 455 ILE cc_start: 0.8789 (mt) cc_final: 0.8252 (mp) REVERT: B 459 LYS cc_start: 0.8692 (mmtt) cc_final: 0.7525 (mmtt) REVERT: B 461 MET cc_start: 0.8631 (mtp) cc_final: 0.8177 (ptp) REVERT: B 463 MET cc_start: 0.7217 (mmm) cc_final: 0.6279 (mmm) REVERT: B 471 LEU cc_start: 0.8257 (mm) cc_final: 0.7984 (mm) REVERT: B 473 LYS cc_start: 0.8311 (mttp) cc_final: 0.7479 (pttt) REVERT: B 476 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8190 (mtpp) REVERT: B 477 THR cc_start: 0.8031 (m) cc_final: 0.7679 (p) REVERT: B 482 TRP cc_start: 0.8409 (t60) cc_final: 0.8039 (t60) REVERT: B 484 PHE cc_start: 0.8361 (t80) cc_final: 0.7776 (t80) REVERT: B 488 MET cc_start: 0.7690 (tpp) cc_final: 0.6505 (tpp) REVERT: B 491 ILE cc_start: 0.8982 (mt) cc_final: 0.8700 (mm) REVERT: B 492 LEU cc_start: 0.8667 (mt) cc_final: 0.7328 (mt) REVERT: B 496 LEU cc_start: 0.7817 (mt) cc_final: 0.7478 (mm) REVERT: B 512 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8125 (mtm-85) REVERT: B 514 GLN cc_start: 0.8822 (tt0) cc_final: 0.8328 (tp40) REVERT: B 537 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7737 (mtmm) REVERT: B 549 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7304 (ptm-80) REVERT: B 563 LYS cc_start: 0.8968 (tppt) cc_final: 0.8122 (tppt) REVERT: B 577 VAL cc_start: 0.8893 (m) cc_final: 0.8660 (p) REVERT: B 578 TYR cc_start: 0.8210 (t80) cc_final: 0.7405 (t80) REVERT: B 582 LEU cc_start: 0.8996 (mt) cc_final: 0.8664 (mm) REVERT: B 656 HIS cc_start: 0.7450 (m90) cc_final: 0.7191 (m90) REVERT: B 674 ARG cc_start: 0.8864 (ttm110) cc_final: 0.8359 (ttm110) REVERT: B 677 ARG cc_start: 0.8524 (ttt180) cc_final: 0.7880 (ttm-80) REVERT: B 678 MET cc_start: 0.8148 (mmm) cc_final: 0.7801 (mmm) REVERT: B 682 GLU cc_start: 0.8220 (tp30) cc_final: 0.7532 (tp30) REVERT: B 691 TYR cc_start: 0.7622 (m-80) cc_final: 0.6939 (m-80) REVERT: B 716 ASP cc_start: 0.8221 (p0) cc_final: 0.7580 (t0) REVERT: B 720 LEU cc_start: 0.9189 (mp) cc_final: 0.8856 (mp) REVERT: B 727 LEU cc_start: 0.8921 (mt) cc_final: 0.7499 (mt) REVERT: B 730 GLN cc_start: 0.8888 (tt0) cc_final: 0.8469 (pp30) REVERT: B 731 ASN cc_start: 0.8509 (p0) cc_final: 0.7683 (p0) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1164 time to fit residues: 55.7313 Evaluate side-chains 337 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 chunk 35 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 382 ASN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN A 567 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092814 restraints weight = 26306.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096199 restraints weight = 15926.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098596 restraints weight = 10824.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100353 restraints weight = 7945.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101613 restraints weight = 6225.566| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10395 Z= 0.128 Angle : 0.643 9.655 14128 Z= 0.326 Chirality : 0.043 0.329 1716 Planarity : 0.004 0.056 1757 Dihedral : 4.138 21.177 1415 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1319 helix: 0.63 (0.18), residues: 830 sheet: -1.32 (1.00), residues: 33 loop : -2.37 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 586 TYR 0.016 0.001 TYR B 377 PHE 0.029 0.001 PHE B 203 TRP 0.021 0.002 TRP B 74 HIS 0.014 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00285 (10395) covalent geometry : angle 0.64337 (14128) hydrogen bonds : bond 0.03649 ( 546) hydrogen bonds : angle 3.83003 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.46 seconds wall clock time: 33 minutes 7.50 seconds (1987.50 seconds total)