Starting phenix.real_space_refine on Fri Feb 14 14:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_32580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_32580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_32580.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_32580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlb_32580/02_2025/7wlb_32580.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.42, per 1000 atoms: 0.63 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: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.99 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: 2.89 Time building geometry restraints manager: 3.32 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.880 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- 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= 0.107 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.000 TRP B 83 HIS 0.001 0.000 HIS A 656 PHE 0.006 0.001 PHE A 115 TYR 0.005 0.001 TYR A 377 ARG 0.001 0.000 ARG A 512 *********************** 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 : 1.150 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: 0.6282 (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: 0.8387 (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: 0.8607 (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: 0.8744 (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: 0.8002 (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: 0.2888 time to fit residues: 163.5793 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 : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 119 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.117749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095573 restraints weight = 25990.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099088 restraints weight = 15466.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101521 restraints weight = 10367.316| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10395 Z= 0.243 Angle : 0.642 11.114 14128 Z= 0.336 Chirality : 0.043 0.217 1716 Planarity : 0.005 0.047 1757 Dihedral : 3.504 17.437 1415 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1319 helix: -0.59 (0.17), residues: 832 sheet: -2.42 (0.89), residues: 33 loop : -3.11 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 74 HIS 0.003 0.001 HIS A 535 PHE 0.023 0.001 PHE A 203 TYR 0.011 0.001 TYR B 377 ARG 0.005 0.001 ARG B 213 *********************** 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 374 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.031 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 38 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7665 (ttm110) REVERT: A 66 LYS cc_start: 0.8788 (tppt) cc_final: 0.8577 (tppt) REVERT: A 96 LEU cc_start: 0.8920 (mt) cc_final: 0.8565 (pp) REVERT: A 100 LEU cc_start: 0.8849 (mm) cc_final: 0.8542 (mm) REVERT: A 105 TYR cc_start: 0.8563 (m-80) cc_final: 0.8331 (m-80) REVERT: A 119 SER cc_start: 0.8779 (t) cc_final: 0.8141 (p) REVERT: A 198 ILE cc_start: 0.8566 (mt) cc_final: 0.8357 (tp) REVERT: A 211 ILE cc_start: 0.8817 (tt) cc_final: 0.8571 (tp) REVERT: A 230 GLN cc_start: 0.8925 (mt0) cc_final: 0.8401 (tp-100) REVERT: A 235 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8025 (mt0) REVERT: A 237 LYS cc_start: 0.8935 (pttm) cc_final: 0.8487 (pttm) REVERT: A 251 LEU cc_start: 0.8001 (mt) cc_final: 0.6979 (mm) REVERT: A 252 SER cc_start: 0.8074 (p) cc_final: 0.7526 (m) REVERT: A 255 TYR cc_start: 0.8020 (m-10) cc_final: 0.7626 (m-10) REVERT: A 263 ASN cc_start: 0.8942 (t0) cc_final: 0.8642 (t0) REVERT: A 276 LEU cc_start: 0.8746 (pp) cc_final: 0.8521 (pp) REVERT: A 282 CYS cc_start: 0.8782 (t) cc_final: 0.8307 (p) REVERT: A 283 MET cc_start: 0.7893 (mmp) cc_final: 0.7656 (mmp) REVERT: A 286 LYS cc_start: 0.9136 (tppt) cc_final: 0.8651 (tppt) REVERT: A 293 LYS cc_start: 0.8085 (tppt) cc_final: 0.7754 (tppt) REVERT: A 303 GLU cc_start: 0.8620 (pm20) cc_final: 0.8403 (pm20) REVERT: A 305 ILE cc_start: 0.8677 (tp) cc_final: 0.8394 (tp) REVERT: A 306 VAL cc_start: 0.8991 (p) cc_final: 0.8656 (m) REVERT: A 309 ILE cc_start: 0.8868 (tp) cc_final: 0.8582 (pt) REVERT: A 321 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8090 (ptmm) REVERT: A 324 ASN cc_start: 0.8188 (t0) cc_final: 0.7715 (t0) REVERT: A 349 MET cc_start: 0.7295 (mtm) cc_final: 0.6923 (mtm) REVERT: A 354 PHE cc_start: 0.8832 (t80) cc_final: 0.8599 (t80) REVERT: A 369 LYS cc_start: 0.8744 (mmtt) cc_final: 0.7929 (mmtt) REVERT: A 371 TYR cc_start: 0.8390 (m-80) cc_final: 0.7786 (m-80) REVERT: A 382 ASN cc_start: 0.8943 (m110) cc_final: 0.8706 (m110) REVERT: A 384 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 385 PHE cc_start: 0.8284 (t80) cc_final: 0.7449 (t80) REVERT: A 394 PHE cc_start: 0.8315 (t80) cc_final: 0.7568 (t80) REVERT: A 401 PHE cc_start: 0.7864 (p90) cc_final: 0.7541 (p90) REVERT: A 414 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 432 MET cc_start: 0.8203 (tpt) cc_final: 0.7871 (tpt) REVERT: A 438 LEU cc_start: 0.8763 (tt) cc_final: 0.8518 (tt) REVERT: A 443 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 454 VAL cc_start: 0.9023 (t) cc_final: 0.8081 (t) REVERT: A 458 LEU cc_start: 0.8750 (mt) cc_final: 0.8450 (mt) REVERT: A 459 LYS cc_start: 0.8488 (tppp) cc_final: 0.6474 (tppp) REVERT: A 463 MET cc_start: 0.7921 (mmp) cc_final: 0.6566 (mmp) REVERT: A 473 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8412 (mtpt) REVERT: A 476 LYS cc_start: 0.8885 (mttm) cc_final: 0.8578 (mttt) REVERT: A 478 ASP cc_start: 0.8217 (m-30) cc_final: 0.8006 (m-30) REVERT: A 486 CYS cc_start: 0.8745 (t) cc_final: 0.8271 (p) REVERT: A 487 ILE cc_start: 0.9069 (mt) cc_final: 0.8700 (pt) REVERT: A 514 GLN cc_start: 0.8404 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 530 TYR cc_start: 0.8367 (m-10) cc_final: 0.7993 (m-10) REVERT: A 535 HIS cc_start: 0.7309 (m90) cc_final: 0.7018 (m-70) REVERT: A 537 LYS cc_start: 0.8638 (tttt) cc_final: 0.8134 (tttt) REVERT: A 549 ARG cc_start: 0.7752 (ttt90) cc_final: 0.6847 (ttm-80) REVERT: A 560 ASP cc_start: 0.8296 (m-30) cc_final: 0.8053 (m-30) REVERT: A 563 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8248 (mmmt) REVERT: A 564 LYS cc_start: 0.8842 (tppt) cc_final: 0.8400 (tppt) REVERT: A 681 LYS cc_start: 0.8076 (tptt) cc_final: 0.7689 (tptt) REVERT: A 687 ASP cc_start: 0.8456 (t0) cc_final: 0.8088 (t0) REVERT: A 701 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 704 GLU cc_start: 0.7448 (tt0) cc_final: 0.7168 (tt0) REVERT: A 705 GLN cc_start: 0.8029 (mm110) cc_final: 0.6864 (mm-40) REVERT: A 715 LYS cc_start: 0.8623 (mttm) cc_final: 0.8203 (ttmm) REVERT: A 724 ASP cc_start: 0.8491 (m-30) cc_final: 0.8017 (m-30) REVERT: A 727 LEU cc_start: 0.9093 (mm) cc_final: 0.8111 (mt) REVERT: A 728 HIS cc_start: 0.8871 (t70) cc_final: 0.8517 (t70) REVERT: A 731 ASN cc_start: 0.8382 (m110) cc_final: 0.8071 (m110) REVERT: B 27 TYR cc_start: 0.8647 (m-10) cc_final: 0.7833 (m-10) REVERT: B 37 GLU cc_start: 0.8059 (pp20) cc_final: 0.7586 (pp20) REVERT: B 122 PHE cc_start: 0.8087 (m-80) cc_final: 0.7574 (m-80) REVERT: B 124 ILE cc_start: 0.8657 (mm) cc_final: 0.8266 (pt) REVERT: B 125 LEU cc_start: 0.8708 (mt) cc_final: 0.8390 (mt) REVERT: B 144 VAL cc_start: 0.8676 (p) cc_final: 0.8343 (m) REVERT: B 147 MET cc_start: 0.8951 (mtt) cc_final: 0.8641 (mtt) REVERT: B 213 ARG cc_start: 0.7567 (mtp85) cc_final: 0.6901 (mtp85) REVERT: B 230 GLN cc_start: 0.8417 (tp40) cc_final: 0.7796 (tp40) REVERT: B 233 VAL cc_start: 0.9110 (p) cc_final: 0.8888 (m) REVERT: B 237 LYS cc_start: 0.8901 (pttt) cc_final: 0.8421 (pttp) REVERT: B 238 ILE cc_start: 0.8724 (tp) cc_final: 0.8246 (pt) REVERT: B 245 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8184 (mtmm) REVERT: B 250 ILE cc_start: 0.8610 (pt) cc_final: 0.8385 (tp) REVERT: B 251 LEU cc_start: 0.8544 (mm) cc_final: 0.6648 (mm) REVERT: B 254 ILE cc_start: 0.8577 (mm) cc_final: 0.7958 (tp) REVERT: B 255 TYR cc_start: 0.7566 (m-10) cc_final: 0.6863 (m-80) REVERT: B 286 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8874 (mttt) REVERT: B 319 LEU cc_start: 0.8675 (mt) cc_final: 0.8142 (pp) REVERT: B 323 TYR cc_start: 0.8094 (m-80) cc_final: 0.7811 (m-80) REVERT: B 356 ILE cc_start: 0.8254 (mt) cc_final: 0.7953 (mp) REVERT: B 440 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7908 (mtt-85) REVERT: B 446 GLN cc_start: 0.8317 (tt0) cc_final: 0.7911 (tt0) REVERT: B 455 ILE cc_start: 0.8652 (mt) cc_final: 0.7742 (mp) REVERT: B 459 LYS cc_start: 0.8713 (mmtt) cc_final: 0.7665 (mmtt) REVERT: B 463 MET cc_start: 0.7111 (mmm) cc_final: 0.6208 (mmm) REVERT: B 477 THR cc_start: 0.8359 (m) cc_final: 0.8061 (p) REVERT: B 482 TRP cc_start: 0.8312 (t60) cc_final: 0.8093 (t60) REVERT: B 484 PHE cc_start: 0.8546 (t80) cc_final: 0.7943 (t80) REVERT: B 488 MET cc_start: 0.7730 (tpp) cc_final: 0.6559 (tpp) REVERT: B 491 ILE cc_start: 0.8879 (mt) cc_final: 0.8501 (mm) REVERT: B 492 LEU cc_start: 0.8745 (mt) cc_final: 0.7446 (mt) REVERT: B 494 LEU cc_start: 0.9077 (mt) cc_final: 0.8721 (mm) REVERT: B 495 ASP cc_start: 0.7469 (p0) cc_final: 0.6865 (p0) REVERT: B 496 LEU cc_start: 0.8020 (mt) cc_final: 0.7210 (mt) REVERT: B 512 ARG cc_start: 0.8624 (mtm180) cc_final: 0.8240 (mtm-85) REVERT: B 514 GLN cc_start: 0.8932 (tt0) cc_final: 0.8462 (tm-30) REVERT: B 535 HIS cc_start: 0.7746 (m-70) cc_final: 0.7351 (m-70) REVERT: B 537 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7639 (mtmm) REVERT: B 563 LYS cc_start: 0.9027 (tppt) cc_final: 0.8202 (tppt) REVERT: B 580 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8317 (mmmt) REVERT: B 590 LYS cc_start: 0.8446 (pttm) cc_final: 0.7924 (pttm) REVERT: B 655 ILE cc_start: 0.8885 (mt) cc_final: 0.8671 (tt) REVERT: B 666 SER cc_start: 0.8734 (p) cc_final: 0.8468 (p) REVERT: B 673 VAL cc_start: 0.9058 (t) cc_final: 0.8711 (t) REVERT: B 677 ARG cc_start: 0.8625 (ttt180) cc_final: 0.8169 (mtp85) REVERT: B 678 MET cc_start: 0.8123 (mmm) cc_final: 0.7742 (mmm) REVERT: B 682 GLU cc_start: 0.8458 (tp30) cc_final: 0.8005 (tp30) REVERT: B 684 GLN cc_start: 0.9176 (tp40) cc_final: 0.8816 (tp40) REVERT: B 702 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7560 (tptp) REVERT: B 705 GLN cc_start: 0.8428 (tt0) cc_final: 0.8165 (tt0) REVERT: B 716 ASP cc_start: 0.8107 (t0) cc_final: 0.7898 (p0) REVERT: B 720 LEU cc_start: 0.8983 (mp) cc_final: 0.8688 (mt) REVERT: B 727 LEU cc_start: 0.8932 (mt) cc_final: 0.8652 (mt) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2806 time to fit residues: 136.6900 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 : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 383 GLN A 728 HIS B 33 GLN B 160 HIS B 207 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094349 restraints weight = 26168.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097847 restraints weight = 15828.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100295 restraints weight = 10710.513| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3648 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= 0.198 Angle : 0.596 12.047 14128 Z= 0.306 Chirality : 0.042 0.235 1716 Planarity : 0.005 0.107 1757 Dihedral : 3.722 21.968 1415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1319 helix: 0.00 (0.18), residues: 824 sheet: -2.22 (0.83), residues: 41 loop : -2.81 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 74 HIS 0.003 0.001 HIS A 723 PHE 0.026 0.001 PHE A 115 TYR 0.017 0.001 TYR A 27 ARG 0.014 0.001 ARG A 440 *********************** 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 369 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.065 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: A 96 LEU cc_start: 0.8893 (mt) cc_final: 0.8608 (mm) REVERT: A 103 MET cc_start: 0.8398 (mtm) cc_final: 0.7634 (mtm) REVERT: A 105 TYR cc_start: 0.8639 (m-80) cc_final: 0.8154 (m-80) REVERT: A 119 SER cc_start: 0.8770 (t) cc_final: 0.8100 (p) REVERT: A 121 PHE cc_start: 0.7706 (t80) cc_final: 0.7494 (t80) REVERT: A 211 ILE cc_start: 0.8902 (tt) cc_final: 0.8604 (tp) REVERT: A 230 GLN cc_start: 0.8904 (mt0) cc_final: 0.8210 (mt0) REVERT: A 237 LYS cc_start: 0.8922 (pttp) cc_final: 0.8587 (pttp) REVERT: A 251 LEU cc_start: 0.8000 (mt) cc_final: 0.6969 (mm) REVERT: A 252 SER cc_start: 0.8063 (p) cc_final: 0.7499 (m) REVERT: A 255 TYR cc_start: 0.8070 (m-10) cc_final: 0.7660 (m-10) REVERT: A 262 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 272 PHE cc_start: 0.8150 (t80) cc_final: 0.7765 (t80) REVERT: A 276 LEU cc_start: 0.8741 (pp) cc_final: 0.8469 (pp) REVERT: A 279 ILE cc_start: 0.9187 (mm) cc_final: 0.8738 (mm) REVERT: A 282 CYS cc_start: 0.8811 (t) cc_final: 0.8334 (p) REVERT: A 283 MET cc_start: 0.7869 (mmp) cc_final: 0.7576 (mmp) REVERT: A 286 LYS cc_start: 0.9147 (tppt) cc_final: 0.8605 (tppt) REVERT: A 293 LYS cc_start: 0.8126 (tppt) cc_final: 0.7768 (tppt) REVERT: A 305 ILE cc_start: 0.8683 (tp) cc_final: 0.8425 (tp) REVERT: A 306 VAL cc_start: 0.8928 (p) cc_final: 0.8549 (m) REVERT: A 309 ILE cc_start: 0.8911 (tp) cc_final: 0.8616 (pt) REVERT: A 315 TYR cc_start: 0.8104 (t80) cc_final: 0.7849 (t80) REVERT: A 321 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8125 (ptmm) REVERT: A 324 ASN cc_start: 0.8253 (t0) cc_final: 0.7744 (t0) REVERT: A 349 MET cc_start: 0.7318 (mtm) cc_final: 0.6925 (mtm) REVERT: A 353 SER cc_start: 0.9010 (m) cc_final: 0.8693 (p) REVERT: A 369 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8517 (tppt) REVERT: A 371 TYR cc_start: 0.8334 (m-80) cc_final: 0.7743 (m-80) REVERT: A 382 ASN cc_start: 0.8933 (m110) cc_final: 0.8652 (t0) REVERT: A 384 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 385 PHE cc_start: 0.8234 (t80) cc_final: 0.7518 (t80) REVERT: A 388 PHE cc_start: 0.9005 (m-80) cc_final: 0.8622 (m-80) REVERT: A 392 ASN cc_start: 0.9255 (m-40) cc_final: 0.8931 (m-40) REVERT: A 394 PHE cc_start: 0.8305 (t80) cc_final: 0.7587 (t80) REVERT: A 397 PHE cc_start: 0.7887 (t80) cc_final: 0.7599 (t80) REVERT: A 409 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7819 (mtm180) REVERT: A 432 MET cc_start: 0.8136 (tpt) cc_final: 0.7846 (tpt) REVERT: A 443 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 454 VAL cc_start: 0.9016 (t) cc_final: 0.8625 (t) REVERT: A 458 LEU cc_start: 0.8874 (mt) cc_final: 0.8569 (mt) REVERT: A 459 LYS cc_start: 0.8455 (tppp) cc_final: 0.6421 (tppp) REVERT: A 461 MET cc_start: 0.8903 (mtm) cc_final: 0.8698 (ptp) REVERT: A 462 PHE cc_start: 0.8446 (m-80) cc_final: 0.7935 (m-80) REVERT: A 463 MET cc_start: 0.7904 (mmp) cc_final: 0.6689 (mmp) REVERT: A 470 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7250 (ptt-90) REVERT: A 473 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8580 (pttp) REVERT: A 474 GLN cc_start: 0.7834 (mt0) cc_final: 0.7532 (mt0) REVERT: A 476 LYS cc_start: 0.8778 (mttm) cc_final: 0.8477 (mmtt) REVERT: A 478 ASP cc_start: 0.8250 (m-30) cc_final: 0.8026 (m-30) REVERT: A 486 CYS cc_start: 0.8814 (t) cc_final: 0.8271 (p) REVERT: A 487 ILE cc_start: 0.8950 (mt) cc_final: 0.8630 (pt) REVERT: A 488 MET cc_start: 0.7954 (mmp) cc_final: 0.7746 (mmp) REVERT: A 496 LEU cc_start: 0.8870 (tp) cc_final: 0.8609 (tp) REVERT: A 530 TYR cc_start: 0.8371 (m-10) cc_final: 0.8158 (m-10) REVERT: A 535 HIS cc_start: 0.7435 (m90) cc_final: 0.7088 (m170) REVERT: A 549 ARG cc_start: 0.7798 (ttt90) cc_final: 0.6865 (ttm-80) REVERT: A 563 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8243 (mmmt) REVERT: A 564 LYS cc_start: 0.8878 (tppt) cc_final: 0.8432 (tppt) REVERT: A 580 LYS cc_start: 0.7976 (tttt) cc_final: 0.7151 (tttp) REVERT: A 677 ARG cc_start: 0.8258 (ttt180) cc_final: 0.7788 (tpp80) REVERT: A 678 MET cc_start: 0.7933 (mmm) cc_final: 0.7678 (mmm) REVERT: A 687 ASP cc_start: 0.8549 (t0) cc_final: 0.8166 (t0) REVERT: A 696 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 697 ASP cc_start: 0.8617 (m-30) cc_final: 0.7810 (p0) REVERT: A 701 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 704 GLU cc_start: 0.7485 (tt0) cc_final: 0.7181 (tt0) REVERT: A 715 LYS cc_start: 0.8497 (mttm) cc_final: 0.8277 (mtpp) REVERT: A 723 HIS cc_start: 0.8248 (t70) cc_final: 0.7985 (t-90) REVERT: A 724 ASP cc_start: 0.8523 (m-30) cc_final: 0.8310 (m-30) REVERT: A 727 LEU cc_start: 0.8861 (mm) cc_final: 0.7988 (mt) REVERT: A 731 ASN cc_start: 0.8569 (m110) cc_final: 0.8061 (m-40) REVERT: B 27 TYR cc_start: 0.8679 (m-10) cc_final: 0.7939 (m-10) REVERT: B 37 GLU cc_start: 0.8087 (pp20) cc_final: 0.7854 (pp20) REVERT: B 39 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7940 (mtp180) REVERT: B 105 TYR cc_start: 0.7333 (m-80) cc_final: 0.6843 (m-80) REVERT: B 122 PHE cc_start: 0.8116 (m-80) cc_final: 0.7593 (m-80) REVERT: B 124 ILE cc_start: 0.8662 (mm) cc_final: 0.8249 (pt) REVERT: B 125 LEU cc_start: 0.8743 (mt) cc_final: 0.8389 (mt) REVERT: B 144 VAL cc_start: 0.8621 (p) cc_final: 0.8117 (m) REVERT: B 147 MET cc_start: 0.8991 (mtt) cc_final: 0.8670 (mtt) REVERT: B 199 ILE cc_start: 0.8509 (tp) cc_final: 0.8305 (tp) REVERT: B 200 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8343 (mt0) REVERT: B 207 GLN cc_start: 0.8723 (tt0) cc_final: 0.8488 (tm-30) REVERT: B 230 GLN cc_start: 0.8424 (tp40) cc_final: 0.7908 (tp40) REVERT: B 233 VAL cc_start: 0.9119 (p) cc_final: 0.8761 (m) REVERT: B 236 LEU cc_start: 0.8835 (tp) cc_final: 0.8015 (mt) REVERT: B 237 LYS cc_start: 0.9030 (pttt) cc_final: 0.8277 (pttp) REVERT: B 241 ASN cc_start: 0.8040 (m110) cc_final: 0.7518 (m-40) REVERT: B 250 ILE cc_start: 0.8680 (pt) cc_final: 0.8350 (tp) REVERT: B 251 LEU cc_start: 0.8613 (mm) cc_final: 0.6563 (mm) REVERT: B 254 ILE cc_start: 0.8529 (mm) cc_final: 0.7994 (tp) REVERT: B 255 TYR cc_start: 0.7526 (m-10) cc_final: 0.6792 (m-80) REVERT: B 259 GLU cc_start: 0.8727 (tt0) cc_final: 0.8305 (tm-30) REVERT: B 260 ILE cc_start: 0.9211 (mm) cc_final: 0.8926 (mt) REVERT: B 263 ASN cc_start: 0.8167 (p0) cc_final: 0.7622 (p0) REVERT: B 280 ILE cc_start: 0.8425 (mm) cc_final: 0.8210 (mm) REVERT: B 283 MET cc_start: 0.8096 (ptp) cc_final: 0.7736 (ptp) REVERT: B 303 GLU cc_start: 0.8963 (mp0) cc_final: 0.8681 (mp0) REVERT: B 319 LEU cc_start: 0.8650 (mt) cc_final: 0.8249 (mt) REVERT: B 323 TYR cc_start: 0.8173 (m-80) cc_final: 0.7832 (m-80) REVERT: B 356 ILE cc_start: 0.8223 (mt) cc_final: 0.7935 (mp) REVERT: B 440 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7824 (mmm160) REVERT: B 443 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6683 (tm-30) REVERT: B 446 GLN cc_start: 0.8362 (tt0) cc_final: 0.8120 (tt0) REVERT: B 450 LEU cc_start: 0.7679 (tp) cc_final: 0.7477 (tp) REVERT: B 455 ILE cc_start: 0.8708 (mt) cc_final: 0.8088 (mp) REVERT: B 459 LYS cc_start: 0.8607 (mmtt) cc_final: 0.7466 (mmtt) REVERT: B 463 MET cc_start: 0.7187 (mmm) cc_final: 0.6241 (mmm) REVERT: B 482 TRP cc_start: 0.8353 (t60) cc_final: 0.8095 (t60) REVERT: B 484 PHE cc_start: 0.8475 (t80) cc_final: 0.7894 (t80) REVERT: B 488 MET cc_start: 0.7755 (tpp) cc_final: 0.6522 (tpp) REVERT: B 491 ILE cc_start: 0.8938 (mt) cc_final: 0.8545 (mm) REVERT: B 492 LEU cc_start: 0.8687 (mt) cc_final: 0.7362 (mt) REVERT: B 494 LEU cc_start: 0.9145 (mt) cc_final: 0.8566 (tt) REVERT: B 495 ASP cc_start: 0.7399 (p0) cc_final: 0.7014 (p0) REVERT: B 496 LEU cc_start: 0.7897 (mt) cc_final: 0.7075 (mt) REVERT: B 512 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8201 (mtm-85) REVERT: B 514 GLN cc_start: 0.8917 (tt0) cc_final: 0.8421 (tm-30) REVERT: B 526 SER cc_start: 0.8900 (m) cc_final: 0.8679 (p) REVERT: B 535 HIS cc_start: 0.7720 (m90) cc_final: 0.7048 (m90) REVERT: B 537 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7616 (mtmm) REVERT: B 563 LYS cc_start: 0.9011 (tppt) cc_final: 0.8185 (tppt) REVERT: B 577 VAL cc_start: 0.9010 (m) cc_final: 0.8758 (p) REVERT: B 578 TYR cc_start: 0.7932 (t80) cc_final: 0.6272 (t80) REVERT: B 580 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8263 (mmmt) REVERT: B 586 ARG cc_start: 0.8401 (ppt170) cc_final: 0.8183 (ttp80) REVERT: B 677 ARG cc_start: 0.8636 (ttt180) cc_final: 0.7999 (ttm-80) REVERT: B 678 MET cc_start: 0.8190 (mmm) cc_final: 0.7810 (mmm) REVERT: B 682 GLU cc_start: 0.8408 (tp30) cc_final: 0.7870 (tp30) REVERT: B 684 GLN cc_start: 0.9178 (tp40) cc_final: 0.8969 (tp-100) REVERT: B 685 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7607 (mtm180) REVERT: B 701 GLU cc_start: 0.7832 (mp0) cc_final: 0.7407 (mp0) REVERT: B 705 GLN cc_start: 0.8601 (tt0) cc_final: 0.8391 (tt0) REVERT: B 720 LEU cc_start: 0.9062 (mp) cc_final: 0.8671 (mt) REVERT: B 724 ASP cc_start: 0.8566 (m-30) cc_final: 0.8275 (m-30) REVERT: B 727 LEU cc_start: 0.8943 (mt) cc_final: 0.8534 (mt) REVERT: B 731 ASN cc_start: 0.8582 (p0) cc_final: 0.8163 (p0) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2796 time to fit residues: 135.2712 Evaluate side-chains 346 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 475 ASN 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 = 0.114637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092224 restraints weight = 25920.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095599 restraints weight = 15691.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097996 restraints weight = 10682.691| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10395 Z= 0.209 Angle : 0.612 12.622 14128 Z= 0.315 Chirality : 0.044 0.420 1716 Planarity : 0.004 0.046 1757 Dihedral : 3.822 21.882 1415 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1319 helix: 0.41 (0.18), residues: 811 sheet: -1.84 (1.00), residues: 34 loop : -2.61 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.005 0.001 HIS A 723 PHE 0.015 0.001 PHE B 385 TYR 0.017 0.001 TYR B 247 ARG 0.009 0.001 ARG B 674 *********************** 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 369 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.072 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 20 TYR cc_start: 0.8459 (t80) cc_final: 0.7933 (t80) REVERT: A 66 LYS cc_start: 0.8863 (tptt) cc_final: 0.8646 (tptt) REVERT: A 96 LEU cc_start: 0.8820 (mt) cc_final: 0.8495 (mm) REVERT: A 103 MET cc_start: 0.8343 (mtm) cc_final: 0.7701 (mtm) REVERT: A 105 TYR cc_start: 0.8690 (m-80) cc_final: 0.8160 (m-80) REVERT: A 115 PHE cc_start: 0.8928 (m-10) cc_final: 0.8676 (m-10) REVERT: A 118 TYR cc_start: 0.8206 (m-80) cc_final: 0.7742 (m-80) REVERT: A 119 SER cc_start: 0.8760 (t) cc_final: 0.8192 (p) REVERT: A 121 PHE cc_start: 0.7786 (t80) cc_final: 0.7491 (t80) REVERT: A 161 PHE cc_start: 0.7979 (m-10) cc_final: 0.6939 (m-10) REVERT: A 211 ILE cc_start: 0.8992 (tt) cc_final: 0.8683 (tp) REVERT: A 230 GLN cc_start: 0.8918 (mt0) cc_final: 0.8377 (tp-100) REVERT: A 251 LEU cc_start: 0.8087 (mt) cc_final: 0.7052 (mm) REVERT: A 252 SER cc_start: 0.8182 (p) cc_final: 0.7642 (m) REVERT: A 255 TYR cc_start: 0.8044 (m-10) cc_final: 0.7641 (m-10) REVERT: A 262 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 272 PHE cc_start: 0.8116 (t80) cc_final: 0.7758 (t80) REVERT: A 276 LEU cc_start: 0.8762 (pp) cc_final: 0.8485 (pp) REVERT: A 279 ILE cc_start: 0.9127 (mm) cc_final: 0.8825 (tp) REVERT: A 282 CYS cc_start: 0.8762 (t) cc_final: 0.8321 (p) REVERT: A 283 MET cc_start: 0.7752 (mmp) cc_final: 0.7486 (mmp) REVERT: A 285 VAL cc_start: 0.8624 (m) cc_final: 0.8320 (p) REVERT: A 286 LYS cc_start: 0.9090 (tppt) cc_final: 0.8641 (tppt) REVERT: A 293 LYS cc_start: 0.8310 (tppt) cc_final: 0.7830 (tppt) REVERT: A 305 ILE cc_start: 0.8659 (tp) cc_final: 0.8457 (tp) REVERT: A 306 VAL cc_start: 0.8893 (p) cc_final: 0.8536 (m) REVERT: A 309 ILE cc_start: 0.8928 (tp) cc_final: 0.8669 (pt) REVERT: A 321 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8168 (ptmm) REVERT: A 324 ASN cc_start: 0.8287 (t0) cc_final: 0.7890 (t0) REVERT: A 345 LEU cc_start: 0.8509 (mt) cc_final: 0.7723 (mp) REVERT: A 349 MET cc_start: 0.7303 (mtm) cc_final: 0.6944 (mtm) REVERT: A 353 SER cc_start: 0.8996 (m) cc_final: 0.8663 (p) REVERT: A 369 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8548 (tppt) REVERT: A 371 TYR cc_start: 0.8385 (m-80) cc_final: 0.7749 (m-80) REVERT: A 385 PHE cc_start: 0.8163 (t80) cc_final: 0.7381 (t80) REVERT: A 388 PHE cc_start: 0.8991 (m-80) cc_final: 0.8641 (m-80) REVERT: A 394 PHE cc_start: 0.8277 (t80) cc_final: 0.7700 (t80) REVERT: A 397 PHE cc_start: 0.7885 (t80) cc_final: 0.7590 (t80) REVERT: A 432 MET cc_start: 0.8213 (tpt) cc_final: 0.7861 (tpt) REVERT: A 443 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 454 VAL cc_start: 0.9004 (t) cc_final: 0.8620 (t) REVERT: A 459 LYS cc_start: 0.8445 (tppp) cc_final: 0.6624 (tppp) REVERT: A 463 MET cc_start: 0.7964 (mmp) cc_final: 0.6727 (mmp) REVERT: A 470 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7424 (ptt-90) REVERT: A 473 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8561 (pttp) REVERT: A 476 LYS cc_start: 0.8767 (mttm) cc_final: 0.8464 (mmtt) REVERT: A 486 CYS cc_start: 0.8841 (t) cc_final: 0.8290 (p) REVERT: A 487 ILE cc_start: 0.8966 (mt) cc_final: 0.8653 (pt) REVERT: A 496 LEU cc_start: 0.8928 (tp) cc_final: 0.8642 (tp) REVERT: A 514 GLN cc_start: 0.8299 (tt0) cc_final: 0.7658 (tm-30) REVERT: A 530 TYR cc_start: 0.8238 (m-10) cc_final: 0.7925 (m-80) REVERT: A 540 GLU cc_start: 0.7681 (pt0) cc_final: 0.7018 (pm20) REVERT: A 549 ARG cc_start: 0.7788 (ttt90) cc_final: 0.7078 (tpp-160) REVERT: A 560 ASP cc_start: 0.8408 (m-30) cc_final: 0.8126 (m-30) REVERT: A 563 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8264 (mmmt) REVERT: A 564 LYS cc_start: 0.8875 (tppt) cc_final: 0.8410 (tppt) REVERT: A 590 LYS cc_start: 0.8465 (pptt) cc_final: 0.8246 (tmmt) REVERT: A 677 ARG cc_start: 0.8385 (ttt180) cc_final: 0.7879 (tpp80) REVERT: A 678 MET cc_start: 0.8002 (mmm) cc_final: 0.7681 (mmm) REVERT: A 687 ASP cc_start: 0.8570 (t0) cc_final: 0.8161 (t0) REVERT: A 691 TYR cc_start: 0.7579 (m-10) cc_final: 0.7225 (m-80) REVERT: A 697 ASP cc_start: 0.8583 (m-30) cc_final: 0.6902 (t0) REVERT: A 701 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 715 LYS cc_start: 0.8456 (mttm) cc_final: 0.8198 (mtpp) REVERT: A 724 ASP cc_start: 0.8509 (m-30) cc_final: 0.8258 (m-30) REVERT: A 727 LEU cc_start: 0.8787 (mm) cc_final: 0.7875 (mm) REVERT: A 728 HIS cc_start: 0.8864 (t70) cc_final: 0.8498 (t70) REVERT: A 730 GLN cc_start: 0.8398 (pp30) cc_final: 0.8114 (pp30) REVERT: A 731 ASN cc_start: 0.8524 (m110) cc_final: 0.8069 (m110) REVERT: B 27 TYR cc_start: 0.8724 (m-10) cc_final: 0.8022 (m-10) REVERT: B 37 GLU cc_start: 0.8105 (pp20) cc_final: 0.7708 (pp20) REVERT: B 105 TYR cc_start: 0.7279 (m-80) cc_final: 0.6853 (m-80) REVERT: B 122 PHE cc_start: 0.8206 (m-80) cc_final: 0.7697 (m-80) REVERT: B 124 ILE cc_start: 0.8681 (mm) cc_final: 0.8235 (pt) REVERT: B 125 LEU cc_start: 0.8804 (mt) cc_final: 0.8510 (mt) REVERT: B 137 SER cc_start: 0.7881 (t) cc_final: 0.7525 (t) REVERT: B 143 VAL cc_start: 0.7792 (m) cc_final: 0.7400 (m) REVERT: B 144 VAL cc_start: 0.8647 (p) cc_final: 0.8158 (m) REVERT: B 147 MET cc_start: 0.9050 (mtt) cc_final: 0.8725 (mtt) REVERT: B 199 ILE cc_start: 0.8541 (tp) cc_final: 0.8318 (tp) REVERT: B 200 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8342 (mt0) REVERT: B 207 GLN cc_start: 0.8766 (tt0) cc_final: 0.8468 (tm-30) REVERT: B 230 GLN cc_start: 0.8359 (tp40) cc_final: 0.7755 (tp40) REVERT: B 233 VAL cc_start: 0.9093 (p) cc_final: 0.8716 (m) REVERT: B 235 GLN cc_start: 0.8356 (pp30) cc_final: 0.8022 (pp30) REVERT: B 236 LEU cc_start: 0.8815 (tp) cc_final: 0.8110 (mt) REVERT: B 237 LYS cc_start: 0.9036 (pttt) cc_final: 0.8229 (pttp) REVERT: B 238 ILE cc_start: 0.8653 (tp) cc_final: 0.8237 (pt) REVERT: B 241 ASN cc_start: 0.8005 (m110) cc_final: 0.7451 (m110) REVERT: B 250 ILE cc_start: 0.8677 (pt) cc_final: 0.8392 (tp) REVERT: B 251 LEU cc_start: 0.8676 (mm) cc_final: 0.6605 (mm) REVERT: B 255 TYR cc_start: 0.7568 (m-10) cc_final: 0.6947 (m-80) REVERT: B 259 GLU cc_start: 0.8703 (tt0) cc_final: 0.8261 (tm-30) REVERT: B 260 ILE cc_start: 0.9230 (mm) cc_final: 0.8876 (mt) REVERT: B 279 ILE cc_start: 0.8695 (tp) cc_final: 0.8356 (pt) REVERT: B 283 MET cc_start: 0.8134 (ptp) cc_final: 0.7797 (ptp) REVERT: B 303 GLU cc_start: 0.8947 (mp0) cc_final: 0.8649 (pm20) REVERT: B 318 ASN cc_start: 0.8598 (t0) cc_final: 0.7990 (t0) REVERT: B 319 LEU cc_start: 0.8665 (mt) cc_final: 0.8260 (mt) REVERT: B 321 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8313 (ttpp) REVERT: B 322 ASN cc_start: 0.8091 (m-40) cc_final: 0.7710 (t0) REVERT: B 323 TYR cc_start: 0.8090 (m-80) cc_final: 0.6985 (m-80) REVERT: B 440 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7826 (mmm160) REVERT: B 443 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6797 (tm-30) REVERT: B 447 LYS cc_start: 0.9107 (mttt) cc_final: 0.8763 (mttt) REVERT: B 455 ILE cc_start: 0.8625 (mt) cc_final: 0.8249 (mp) REVERT: B 459 LYS cc_start: 0.8732 (mmtt) cc_final: 0.7695 (mmtt) REVERT: B 463 MET cc_start: 0.7269 (mmm) cc_final: 0.6367 (mmm) REVERT: B 477 THR cc_start: 0.8189 (m) cc_final: 0.7817 (p) REVERT: B 482 TRP cc_start: 0.8354 (t60) cc_final: 0.8090 (t60) REVERT: B 484 PHE cc_start: 0.8463 (t80) cc_final: 0.7901 (t80) REVERT: B 488 MET cc_start: 0.7797 (tpp) cc_final: 0.6530 (tpp) REVERT: B 491 ILE cc_start: 0.8935 (mt) cc_final: 0.8589 (mm) REVERT: B 492 LEU cc_start: 0.8709 (mt) cc_final: 0.7286 (mt) REVERT: B 494 LEU cc_start: 0.9143 (mt) cc_final: 0.8674 (tt) REVERT: B 496 LEU cc_start: 0.7982 (mt) cc_final: 0.7651 (mm) REVERT: B 512 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8200 (mtm-85) REVERT: B 514 GLN cc_start: 0.8900 (tt0) cc_final: 0.8415 (tm-30) REVERT: B 537 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7709 (mtmm) REVERT: B 549 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7835 (ttt-90) REVERT: B 563 LYS cc_start: 0.9008 (tppt) cc_final: 0.7937 (tppt) REVERT: B 567 ASN cc_start: 0.8290 (m-40) cc_final: 0.7624 (m110) REVERT: B 577 VAL cc_start: 0.9004 (m) cc_final: 0.8752 (p) REVERT: B 578 TYR cc_start: 0.7924 (t80) cc_final: 0.6175 (t80) REVERT: B 674 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8033 (ttm110) REVERT: B 677 ARG cc_start: 0.8605 (ttt180) cc_final: 0.7931 (ttm-80) REVERT: B 678 MET cc_start: 0.8201 (mmm) cc_final: 0.7820 (mmm) REVERT: B 682 GLU cc_start: 0.8366 (tp30) cc_final: 0.7891 (tp30) REVERT: B 684 GLN cc_start: 0.9164 (tp40) cc_final: 0.8858 (tp40) REVERT: B 685 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7626 (mtm180) REVERT: B 705 GLN cc_start: 0.8612 (tt0) cc_final: 0.8403 (tt0) REVERT: B 719 PHE cc_start: 0.7678 (m-80) cc_final: 0.7344 (m-10) REVERT: B 720 LEU cc_start: 0.9115 (mp) cc_final: 0.8737 (mt) REVERT: B 727 LEU cc_start: 0.8955 (mt) cc_final: 0.8702 (mt) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2857 time to fit residues: 139.3736 Evaluate side-chains 339 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 131 optimal weight: 0.0030 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 730 GLN B 207 GLN B 289 ASN ** B 318 ASN ** 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 = 0.3790 r_free = 0.3790 target = 0.115311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092479 restraints weight = 25712.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095965 restraints weight = 15506.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098389 restraints weight = 10495.342| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4364 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= 0.170 Angle : 0.592 8.646 14128 Z= 0.301 Chirality : 0.042 0.271 1716 Planarity : 0.004 0.047 1757 Dihedral : 3.883 24.035 1415 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1319 helix: 0.60 (0.18), residues: 813 sheet: -1.78 (1.01), residues: 34 loop : -2.45 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.003 0.000 HIS A 723 PHE 0.015 0.001 PHE A 115 TYR 0.008 0.001 TYR A 78 ARG 0.006 0.000 ARG B 674 *********************** 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 367 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 1.152 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: 0.8421 (t80) cc_final: 0.7870 (t80) REVERT: A 38 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7586 (ttm110) REVERT: A 66 LYS cc_start: 0.8866 (tppt) cc_final: 0.8532 (mmmt) REVERT: A 96 LEU cc_start: 0.8808 (mt) cc_final: 0.8431 (mm) REVERT: A 103 MET cc_start: 0.8264 (mtm) cc_final: 0.8051 (mpp) REVERT: A 105 TYR cc_start: 0.8594 (m-80) cc_final: 0.8251 (m-80) REVERT: A 118 TYR cc_start: 0.8162 (m-80) cc_final: 0.7731 (m-80) REVERT: A 119 SER cc_start: 0.8804 (t) cc_final: 0.8204 (p) REVERT: A 121 PHE cc_start: 0.7673 (t80) cc_final: 0.7355 (t80) REVERT: A 161 PHE cc_start: 0.8011 (m-10) cc_final: 0.6891 (m-10) REVERT: A 194 LEU cc_start: 0.8465 (tp) cc_final: 0.8182 (mm) REVERT: A 211 ILE cc_start: 0.8979 (tt) cc_final: 0.8691 (tp) REVERT: A 230 GLN cc_start: 0.8881 (mt0) cc_final: 0.8355 (tp-100) REVERT: A 235 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8340 (mm-40) REVERT: A 237 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8676 (pttm) REVERT: A 251 LEU cc_start: 0.8012 (mt) cc_final: 0.6936 (mm) REVERT: A 252 SER cc_start: 0.8135 (p) cc_final: 0.7598 (m) REVERT: A 255 TYR cc_start: 0.8024 (m-10) cc_final: 0.7621 (m-10) REVERT: A 262 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 272 PHE cc_start: 0.8092 (t80) cc_final: 0.7705 (t80) REVERT: A 276 LEU cc_start: 0.8753 (pp) cc_final: 0.8460 (pp) REVERT: A 278 THR cc_start: 0.9021 (p) cc_final: 0.8779 (p) REVERT: A 279 ILE cc_start: 0.9116 (mm) cc_final: 0.8716 (tp) REVERT: A 282 CYS cc_start: 0.8775 (t) cc_final: 0.8364 (p) REVERT: A 283 MET cc_start: 0.7768 (mmp) cc_final: 0.7440 (mmp) REVERT: A 285 VAL cc_start: 0.8661 (m) cc_final: 0.8392 (p) REVERT: A 286 LYS cc_start: 0.9047 (tppt) cc_final: 0.8668 (tppt) REVERT: A 293 LYS cc_start: 0.8332 (tppt) cc_final: 0.7853 (tppt) REVERT: A 305 ILE cc_start: 0.8673 (tp) cc_final: 0.8287 (pt) REVERT: A 309 ILE cc_start: 0.8909 (tp) cc_final: 0.8635 (pt) REVERT: A 315 TYR cc_start: 0.8033 (t80) cc_final: 0.7832 (t80) REVERT: A 321 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8173 (ptmm) REVERT: A 324 ASN cc_start: 0.8282 (t0) cc_final: 0.7938 (t0) REVERT: A 345 LEU cc_start: 0.8486 (mt) cc_final: 0.7651 (mp) REVERT: A 349 MET cc_start: 0.7259 (mtm) cc_final: 0.6901 (mtm) REVERT: A 353 SER cc_start: 0.8983 (m) cc_final: 0.8663 (p) REVERT: A 369 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8038 (mmtt) REVERT: A 371 TYR cc_start: 0.8328 (m-80) cc_final: 0.7774 (m-80) REVERT: A 385 PHE cc_start: 0.8109 (t80) cc_final: 0.7322 (t80) REVERT: A 388 PHE cc_start: 0.8968 (m-80) cc_final: 0.8644 (m-80) REVERT: A 394 PHE cc_start: 0.8226 (t80) cc_final: 0.7654 (t80) REVERT: A 397 PHE cc_start: 0.7850 (t80) cc_final: 0.7618 (t80) REVERT: A 414 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 432 MET cc_start: 0.8144 (tpt) cc_final: 0.7808 (tpt) REVERT: A 435 ILE cc_start: 0.8339 (mt) cc_final: 0.8075 (tp) REVERT: A 443 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 454 VAL cc_start: 0.8990 (t) cc_final: 0.8746 (t) REVERT: A 458 LEU cc_start: 0.8601 (mt) cc_final: 0.8373 (mt) REVERT: A 459 LYS cc_start: 0.8445 (tppp) cc_final: 0.6558 (tppp) REVERT: A 463 MET cc_start: 0.8039 (mmp) cc_final: 0.6778 (mmp) REVERT: A 467 ASP cc_start: 0.8022 (p0) cc_final: 0.7816 (p0) REVERT: A 470 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7745 (ptt-90) REVERT: A 473 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8358 (mtpt) REVERT: A 476 LYS cc_start: 0.8762 (mttm) cc_final: 0.8481 (mmtt) REVERT: A 478 ASP cc_start: 0.8259 (m-30) cc_final: 0.8006 (m-30) REVERT: A 486 CYS cc_start: 0.8781 (t) cc_final: 0.8253 (p) REVERT: A 487 ILE cc_start: 0.8947 (mt) cc_final: 0.8622 (pt) REVERT: A 496 LEU cc_start: 0.8943 (tp) cc_final: 0.8639 (tp) REVERT: A 514 GLN cc_start: 0.8272 (tt0) cc_final: 0.7691 (tm-30) REVERT: A 530 TYR cc_start: 0.8232 (m-10) cc_final: 0.7819 (m-80) REVERT: A 540 GLU cc_start: 0.7656 (pt0) cc_final: 0.6999 (pm20) REVERT: A 549 ARG cc_start: 0.7775 (ttt90) cc_final: 0.7081 (tpp-160) REVERT: A 560 ASP cc_start: 0.8405 (m-30) cc_final: 0.8123 (m-30) REVERT: A 563 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8198 (mmmt) REVERT: A 564 LYS cc_start: 0.8870 (tppt) cc_final: 0.8374 (tppt) REVERT: A 583 LYS cc_start: 0.8856 (ptmm) cc_final: 0.8614 (ptmm) REVERT: A 677 ARG cc_start: 0.8360 (ttt180) cc_final: 0.7868 (tpp80) REVERT: A 678 MET cc_start: 0.8068 (mmm) cc_final: 0.7699 (mmm) REVERT: A 682 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 685 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7932 (mtm-85) REVERT: A 687 ASP cc_start: 0.8522 (t0) cc_final: 0.8118 (t0) REVERT: A 697 ASP cc_start: 0.8618 (m-30) cc_final: 0.7649 (p0) REVERT: A 701 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 705 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7592 (tp-100) REVERT: A 715 LYS cc_start: 0.8342 (mttm) cc_final: 0.7839 (mttm) REVERT: A 723 HIS cc_start: 0.8094 (t70) cc_final: 0.7739 (t-90) REVERT: A 724 ASP cc_start: 0.8492 (m-30) cc_final: 0.7979 (m-30) REVERT: A 727 LEU cc_start: 0.8833 (mm) cc_final: 0.7830 (mt) REVERT: A 728 HIS cc_start: 0.8851 (t70) cc_final: 0.8505 (t70) REVERT: A 730 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8146 (pp30) REVERT: A 731 ASN cc_start: 0.8581 (m110) cc_final: 0.8129 (m110) REVERT: B 27 TYR cc_start: 0.8736 (m-10) cc_final: 0.8064 (m-10) REVERT: B 37 GLU cc_start: 0.8042 (pp20) cc_final: 0.7645 (pp20) REVERT: B 105 TYR cc_start: 0.7242 (m-80) cc_final: 0.6891 (m-80) REVERT: B 122 PHE cc_start: 0.8257 (m-80) cc_final: 0.7747 (m-80) REVERT: B 124 ILE cc_start: 0.8714 (mm) cc_final: 0.8327 (pt) REVERT: B 125 LEU cc_start: 0.8797 (mt) cc_final: 0.8527 (mt) REVERT: B 137 SER cc_start: 0.7836 (t) cc_final: 0.7516 (t) REVERT: B 143 VAL cc_start: 0.7812 (m) cc_final: 0.7445 (m) REVERT: B 144 VAL cc_start: 0.8611 (p) cc_final: 0.8114 (m) REVERT: B 147 MET cc_start: 0.9031 (mtt) cc_final: 0.8736 (mtt) REVERT: B 155 MET cc_start: 0.6223 (ptp) cc_final: 0.6004 (ptp) REVERT: B 186 VAL cc_start: 0.9108 (p) cc_final: 0.8856 (m) REVERT: B 199 ILE cc_start: 0.8492 (tp) cc_final: 0.8281 (tp) REVERT: B 207 GLN cc_start: 0.8761 (tt0) cc_final: 0.8432 (tm-30) REVERT: B 230 GLN cc_start: 0.8349 (tp40) cc_final: 0.7764 (tp40) REVERT: B 233 VAL cc_start: 0.9077 (p) cc_final: 0.8608 (m) REVERT: B 235 GLN cc_start: 0.8318 (pp30) cc_final: 0.8051 (pp30) REVERT: B 236 LEU cc_start: 0.8832 (tp) cc_final: 0.8188 (mt) REVERT: B 237 LYS cc_start: 0.8965 (pttt) cc_final: 0.8228 (pttp) REVERT: B 238 ILE cc_start: 0.8648 (tp) cc_final: 0.8438 (tp) REVERT: B 250 ILE cc_start: 0.8679 (pt) cc_final: 0.8373 (tp) REVERT: B 251 LEU cc_start: 0.8629 (mm) cc_final: 0.6596 (mm) REVERT: B 255 TYR cc_start: 0.7582 (m-10) cc_final: 0.6963 (m-80) REVERT: B 259 GLU cc_start: 0.8653 (tt0) cc_final: 0.8308 (tt0) REVERT: B 279 ILE cc_start: 0.8630 (tp) cc_final: 0.8374 (pt) REVERT: B 280 ILE cc_start: 0.8550 (mm) cc_final: 0.8345 (mm) REVERT: B 283 MET cc_start: 0.8137 (ptp) cc_final: 0.7883 (ptp) REVERT: B 303 GLU cc_start: 0.8931 (mp0) cc_final: 0.8617 (pm20) REVERT: B 319 LEU cc_start: 0.8660 (mt) cc_final: 0.8330 (mt) REVERT: B 321 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8150 (ttpp) REVERT: B 323 TYR cc_start: 0.8124 (m-80) cc_final: 0.7800 (m-80) REVERT: B 324 ASN cc_start: 0.8427 (t0) cc_final: 0.8192 (t0) REVERT: B 440 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7847 (mmm160) REVERT: B 443 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6844 (tm-30) REVERT: B 455 ILE cc_start: 0.8618 (mt) cc_final: 0.8085 (mp) REVERT: B 459 LYS cc_start: 0.8745 (mmtt) cc_final: 0.7680 (mmtt) REVERT: B 463 MET cc_start: 0.7255 (mmm) cc_final: 0.6363 (mmm) REVERT: B 477 THR cc_start: 0.8148 (m) cc_final: 0.7758 (p) REVERT: B 478 ASP cc_start: 0.8433 (p0) cc_final: 0.8141 (p0) REVERT: B 482 TRP cc_start: 0.8369 (t60) cc_final: 0.8100 (t60) REVERT: B 484 PHE cc_start: 0.8387 (t80) cc_final: 0.7858 (t80) REVERT: B 488 MET cc_start: 0.7737 (tpp) cc_final: 0.6413 (tpp) REVERT: B 491 ILE cc_start: 0.8907 (mt) cc_final: 0.8560 (mm) REVERT: B 492 LEU cc_start: 0.8638 (mt) cc_final: 0.7288 (mt) REVERT: B 494 LEU cc_start: 0.9170 (mt) cc_final: 0.8591 (tt) REVERT: B 495 ASP cc_start: 0.7427 (p0) cc_final: 0.7117 (p0) REVERT: B 496 LEU cc_start: 0.7947 (mt) cc_final: 0.7179 (mt) REVERT: B 512 ARG cc_start: 0.8569 (mtm180) cc_final: 0.8273 (mtm-85) REVERT: B 514 GLN cc_start: 0.8866 (tt0) cc_final: 0.8401 (tm-30) REVERT: B 537 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7706 (mtmm) REVERT: B 549 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7811 (ttt-90) REVERT: B 563 LYS cc_start: 0.8987 (tppt) cc_final: 0.8143 (tppt) REVERT: B 577 VAL cc_start: 0.9032 (m) cc_final: 0.8734 (p) REVERT: B 586 ARG cc_start: 0.8402 (ppt170) cc_final: 0.8073 (ttp80) REVERT: B 590 LYS cc_start: 0.8332 (pttp) cc_final: 0.8092 (pttm) REVERT: B 592 ILE cc_start: 0.8758 (mm) cc_final: 0.8513 (mm) REVERT: B 594 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8232 (ptpt) REVERT: B 674 ARG cc_start: 0.8876 (ttm110) cc_final: 0.8072 (ttm110) REVERT: B 677 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8103 (ttm-80) REVERT: B 678 MET cc_start: 0.8163 (mmm) cc_final: 0.7793 (mmm) REVERT: B 682 GLU cc_start: 0.8358 (tp30) cc_final: 0.7719 (tp30) REVERT: B 684 GLN cc_start: 0.9146 (tp40) cc_final: 0.8918 (tp-100) REVERT: B 705 GLN cc_start: 0.8643 (tt0) cc_final: 0.8403 (tt0) REVERT: B 716 ASP cc_start: 0.8291 (p0) cc_final: 0.7361 (t0) REVERT: B 719 PHE cc_start: 0.7711 (m-80) cc_final: 0.7419 (m-10) REVERT: B 720 LEU cc_start: 0.9112 (mp) cc_final: 0.8787 (mt) REVERT: B 727 LEU cc_start: 0.8983 (mt) cc_final: 0.8727 (mt) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.2781 time to fit residues: 134.1463 Evaluate side-chains 333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 0.0570 chunk 12 optimal weight: 0.0870 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.116463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093597 restraints weight = 25877.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097046 restraints weight = 15689.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099511 restraints weight = 10704.209| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10395 Z= 0.158 Angle : 0.584 9.249 14128 Z= 0.295 Chirality : 0.042 0.287 1716 Planarity : 0.004 0.049 1757 Dihedral : 3.877 23.402 1415 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1319 helix: 0.63 (0.18), residues: 824 sheet: -1.75 (1.01), residues: 34 loop : -2.40 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 518 HIS 0.006 0.000 HIS A 723 PHE 0.021 0.001 PHE A 115 TYR 0.020 0.001 TYR B 578 ARG 0.005 0.000 ARG A 409 *********************** 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 373 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.148 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 20 TYR cc_start: 0.8434 (t80) cc_final: 0.7970 (t80) REVERT: A 38 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7404 (ttm110) REVERT: A 66 LYS cc_start: 0.8862 (tppt) cc_final: 0.8516 (mmmt) REVERT: A 96 LEU cc_start: 0.8748 (mt) cc_final: 0.8402 (mm) REVERT: A 103 MET cc_start: 0.8268 (mtm) cc_final: 0.7595 (mtt) REVERT: A 105 TYR cc_start: 0.8331 (m-80) cc_final: 0.7971 (m-80) REVERT: A 118 TYR cc_start: 0.8265 (m-80) cc_final: 0.7848 (m-80) REVERT: A 119 SER cc_start: 0.8784 (t) cc_final: 0.8224 (p) REVERT: A 121 PHE cc_start: 0.7657 (t80) cc_final: 0.7339 (t80) REVERT: A 161 PHE cc_start: 0.8028 (m-10) cc_final: 0.6822 (m-10) REVERT: A 194 LEU cc_start: 0.8464 (tp) cc_final: 0.8171 (mm) REVERT: A 211 ILE cc_start: 0.8985 (tt) cc_final: 0.8707 (tp) REVERT: A 230 GLN cc_start: 0.8841 (mt0) cc_final: 0.8221 (mt0) REVERT: A 237 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8672 (pttm) REVERT: A 251 LEU cc_start: 0.7935 (mt) cc_final: 0.6878 (mm) REVERT: A 252 SER cc_start: 0.8115 (p) cc_final: 0.7536 (m) REVERT: A 255 TYR cc_start: 0.8024 (m-10) cc_final: 0.7611 (m-10) REVERT: A 262 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 272 PHE cc_start: 0.8186 (t80) cc_final: 0.7765 (t80) REVERT: A 276 LEU cc_start: 0.8679 (pp) cc_final: 0.8388 (pp) REVERT: A 279 ILE cc_start: 0.9099 (mm) cc_final: 0.8726 (tp) REVERT: A 282 CYS cc_start: 0.8816 (t) cc_final: 0.8380 (p) REVERT: A 283 MET cc_start: 0.7781 (mmp) cc_final: 0.7424 (mmp) REVERT: A 285 VAL cc_start: 0.8659 (m) cc_final: 0.8296 (p) REVERT: A 286 LYS cc_start: 0.9038 (tppt) cc_final: 0.8619 (tppt) REVERT: A 289 ASN cc_start: 0.8828 (m-40) cc_final: 0.8243 (m110) REVERT: A 293 LYS cc_start: 0.8341 (tppt) cc_final: 0.7851 (tppt) REVERT: A 303 GLU cc_start: 0.8682 (pm20) cc_final: 0.8374 (pm20) REVERT: A 305 ILE cc_start: 0.8611 (tp) cc_final: 0.8223 (pt) REVERT: A 309 ILE cc_start: 0.8902 (tp) cc_final: 0.8624 (pt) REVERT: A 321 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8170 (ptmm) REVERT: A 324 ASN cc_start: 0.8329 (t0) cc_final: 0.7976 (t0) REVERT: A 345 LEU cc_start: 0.8496 (mt) cc_final: 0.7648 (mp) REVERT: A 349 MET cc_start: 0.7321 (mtm) cc_final: 0.6946 (mtm) REVERT: A 353 SER cc_start: 0.8976 (m) cc_final: 0.8675 (p) REVERT: A 369 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8101 (mmtt) REVERT: A 371 TYR cc_start: 0.8310 (m-80) cc_final: 0.7754 (m-80) REVERT: A 383 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8452 (mm-40) REVERT: A 385 PHE cc_start: 0.8075 (t80) cc_final: 0.7304 (t80) REVERT: A 388 PHE cc_start: 0.9003 (m-80) cc_final: 0.8730 (m-80) REVERT: A 392 ASN cc_start: 0.9253 (m-40) cc_final: 0.8906 (m-40) REVERT: A 394 PHE cc_start: 0.8253 (t80) cc_final: 0.7630 (t80) REVERT: A 397 PHE cc_start: 0.7872 (t80) cc_final: 0.7635 (t80) REVERT: A 432 MET cc_start: 0.8130 (tpt) cc_final: 0.7809 (tpt) REVERT: A 443 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 454 VAL cc_start: 0.9006 (t) cc_final: 0.8652 (t) REVERT: A 458 LEU cc_start: 0.8621 (mt) cc_final: 0.8421 (mt) REVERT: A 459 LYS cc_start: 0.8369 (tppp) cc_final: 0.6643 (tppp) REVERT: A 462 PHE cc_start: 0.8376 (m-80) cc_final: 0.8065 (m-80) REVERT: A 463 MET cc_start: 0.7960 (mmp) cc_final: 0.6971 (mmp) REVERT: A 470 ARG cc_start: 0.7930 (ptp-170) cc_final: 0.7701 (ptt-90) REVERT: A 473 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8385 (mtpt) REVERT: A 476 LYS cc_start: 0.8753 (mttm) cc_final: 0.8411 (mmtm) REVERT: A 478 ASP cc_start: 0.8260 (m-30) cc_final: 0.8016 (m-30) REVERT: A 486 CYS cc_start: 0.8776 (t) cc_final: 0.8253 (p) REVERT: A 487 ILE cc_start: 0.8927 (mt) cc_final: 0.8573 (pt) REVERT: A 496 LEU cc_start: 0.8933 (tp) cc_final: 0.8621 (tp) REVERT: A 530 TYR cc_start: 0.8195 (m-10) cc_final: 0.7848 (m-80) REVERT: A 531 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7942 (mmpt) REVERT: A 549 ARG cc_start: 0.7804 (ttt90) cc_final: 0.7092 (tpp-160) REVERT: A 560 ASP cc_start: 0.8414 (m-30) cc_final: 0.7950 (m-30) REVERT: A 563 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8193 (mmmt) REVERT: A 564 LYS cc_start: 0.8857 (tppt) cc_final: 0.8409 (tppt) REVERT: A 583 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8626 (ptmm) REVERT: A 677 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7920 (tpp80) REVERT: A 678 MET cc_start: 0.7996 (mmm) cc_final: 0.7618 (mmm) REVERT: A 687 ASP cc_start: 0.8502 (t0) cc_final: 0.8109 (t0) REVERT: A 696 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 697 ASP cc_start: 0.8555 (m-30) cc_final: 0.7762 (p0) REVERT: A 701 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 705 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7545 (tp-100) REVERT: A 715 LYS cc_start: 0.8385 (mttm) cc_final: 0.7916 (mttm) REVERT: A 724 ASP cc_start: 0.8480 (m-30) cc_final: 0.7929 (m-30) REVERT: A 728 HIS cc_start: 0.8855 (t70) cc_final: 0.8521 (t70) REVERT: A 731 ASN cc_start: 0.8619 (m110) cc_final: 0.8191 (m-40) REVERT: B 27 TYR cc_start: 0.8712 (m-10) cc_final: 0.8033 (m-10) REVERT: B 30 LEU cc_start: 0.8514 (pt) cc_final: 0.8112 (pt) REVERT: B 36 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: B 39 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7710 (mtt-85) REVERT: B 105 TYR cc_start: 0.7272 (m-80) cc_final: 0.6969 (m-80) REVERT: B 122 PHE cc_start: 0.8267 (m-80) cc_final: 0.7727 (m-80) REVERT: B 124 ILE cc_start: 0.8677 (mm) cc_final: 0.8214 (pt) REVERT: B 125 LEU cc_start: 0.8745 (mt) cc_final: 0.8462 (mt) REVERT: B 137 SER cc_start: 0.8020 (t) cc_final: 0.7736 (t) REVERT: B 143 VAL cc_start: 0.7815 (m) cc_final: 0.7478 (m) REVERT: B 144 VAL cc_start: 0.8598 (p) cc_final: 0.8084 (m) REVERT: B 147 MET cc_start: 0.9043 (mtt) cc_final: 0.8721 (mtt) REVERT: B 186 VAL cc_start: 0.9121 (p) cc_final: 0.8831 (m) REVERT: B 199 ILE cc_start: 0.8563 (tp) cc_final: 0.8351 (tp) REVERT: B 207 GLN cc_start: 0.8724 (tt0) cc_final: 0.8420 (tm-30) REVERT: B 213 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7425 (mtp180) REVERT: B 230 GLN cc_start: 0.8336 (tp40) cc_final: 0.8036 (pp30) REVERT: B 236 LEU cc_start: 0.8841 (tp) cc_final: 0.8480 (tp) REVERT: B 237 LYS cc_start: 0.8952 (pttt) cc_final: 0.8419 (pttp) REVERT: B 238 ILE cc_start: 0.8637 (tp) cc_final: 0.8423 (tp) REVERT: B 250 ILE cc_start: 0.8667 (pt) cc_final: 0.8371 (tp) REVERT: B 251 LEU cc_start: 0.8578 (mm) cc_final: 0.6579 (mm) REVERT: B 255 TYR cc_start: 0.7613 (m-10) cc_final: 0.6957 (m-80) REVERT: B 259 GLU cc_start: 0.8667 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 260 ILE cc_start: 0.9221 (mm) cc_final: 0.8854 (mt) REVERT: B 303 GLU cc_start: 0.8963 (mp0) cc_final: 0.8628 (pm20) REVERT: B 318 ASN cc_start: 0.8555 (t0) cc_final: 0.7804 (t0) REVERT: B 319 LEU cc_start: 0.8671 (mt) cc_final: 0.8294 (pp) REVERT: B 321 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8292 (ttpp) REVERT: B 322 ASN cc_start: 0.8067 (m-40) cc_final: 0.7694 (t0) REVERT: B 323 TYR cc_start: 0.8105 (m-80) cc_final: 0.7017 (m-80) REVERT: B 440 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7815 (mmm160) REVERT: B 443 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6796 (tm-30) REVERT: B 447 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8426 (ptpt) REVERT: B 455 ILE cc_start: 0.8593 (mt) cc_final: 0.8106 (mp) REVERT: B 459 LYS cc_start: 0.8632 (mmtt) cc_final: 0.7335 (mmtt) REVERT: B 463 MET cc_start: 0.7259 (mmm) cc_final: 0.6350 (mmm) REVERT: B 473 LYS cc_start: 0.8466 (mttp) cc_final: 0.7568 (pttt) REVERT: B 477 THR cc_start: 0.8117 (m) cc_final: 0.7769 (p) REVERT: B 478 ASP cc_start: 0.8440 (p0) cc_final: 0.8177 (p0) REVERT: B 482 TRP cc_start: 0.8358 (t60) cc_final: 0.8133 (t60) REVERT: B 484 PHE cc_start: 0.8395 (t80) cc_final: 0.7859 (t80) REVERT: B 488 MET cc_start: 0.7751 (tpp) cc_final: 0.6424 (tpp) REVERT: B 491 ILE cc_start: 0.8888 (mt) cc_final: 0.8543 (mm) REVERT: B 492 LEU cc_start: 0.8626 (mt) cc_final: 0.7266 (mt) REVERT: B 494 LEU cc_start: 0.9180 (mt) cc_final: 0.8558 (tt) REVERT: B 495 ASP cc_start: 0.7425 (p0) cc_final: 0.7151 (p0) REVERT: B 496 LEU cc_start: 0.7925 (mt) cc_final: 0.7133 (mt) REVERT: B 512 ARG cc_start: 0.8563 (mtm180) cc_final: 0.8181 (mtm-85) REVERT: B 514 GLN cc_start: 0.8889 (tt0) cc_final: 0.8400 (tm-30) REVERT: B 563 LYS cc_start: 0.9020 (tppt) cc_final: 0.7949 (tppt) REVERT: B 567 ASN cc_start: 0.8259 (m-40) cc_final: 0.7794 (m110) REVERT: B 577 VAL cc_start: 0.8977 (m) cc_final: 0.8734 (p) REVERT: B 580 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8300 (mmmt) REVERT: B 586 ARG cc_start: 0.8369 (ppt170) cc_final: 0.7999 (ttp80) REVERT: B 674 ARG cc_start: 0.8876 (ttm110) cc_final: 0.8095 (ttm110) REVERT: B 677 ARG cc_start: 0.8599 (ttt180) cc_final: 0.7951 (ttm-80) REVERT: B 678 MET cc_start: 0.8201 (mmm) cc_final: 0.7822 (mmm) REVERT: B 682 GLU cc_start: 0.8291 (tp30) cc_final: 0.7715 (tp30) REVERT: B 694 LEU cc_start: 0.8063 (pt) cc_final: 0.7796 (pp) REVERT: B 703 MET cc_start: 0.8375 (mtm) cc_final: 0.7764 (mtm) REVERT: B 705 GLN cc_start: 0.8621 (tt0) cc_final: 0.8291 (pp30) REVERT: B 716 ASP cc_start: 0.8280 (p0) cc_final: 0.7397 (t0) REVERT: B 719 PHE cc_start: 0.7830 (m-80) cc_final: 0.7547 (m-10) REVERT: B 720 LEU cc_start: 0.9131 (mp) cc_final: 0.8770 (mt) REVERT: B 727 LEU cc_start: 0.8947 (mt) cc_final: 0.7511 (mt) REVERT: B 730 GLN cc_start: 0.8926 (tt0) cc_final: 0.8440 (pp30) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2797 time to fit residues: 137.7560 Evaluate side-chains 340 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 474 GLN B 207 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.114726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091745 restraints weight = 26256.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095166 restraints weight = 15961.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097634 restraints weight = 10931.915| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10395 Z= 0.198 Angle : 0.613 9.244 14128 Z= 0.316 Chirality : 0.044 0.304 1716 Planarity : 0.004 0.050 1757 Dihedral : 3.913 22.535 1415 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1319 helix: 0.62 (0.19), residues: 821 sheet: -1.74 (1.01), residues: 34 loop : -2.29 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 518 HIS 0.003 0.000 HIS A 723 PHE 0.029 0.001 PHE A 115 TYR 0.043 0.001 TYR B 578 ARG 0.008 0.001 ARG B 38 *********************** 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 354 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.113 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: 0.8466 (t80) cc_final: 0.8052 (t80) REVERT: A 38 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7633 (ttm110) REVERT: A 66 LYS cc_start: 0.8911 (tppt) cc_final: 0.8625 (tppt) REVERT: A 96 LEU cc_start: 0.8683 (mt) cc_final: 0.8323 (mm) REVERT: A 103 MET cc_start: 0.8456 (mtm) cc_final: 0.7831 (mtm) REVERT: A 105 TYR cc_start: 0.8588 (m-80) cc_final: 0.8250 (m-80) REVERT: A 118 TYR cc_start: 0.8297 (m-80) cc_final: 0.7939 (m-80) REVERT: A 119 SER cc_start: 0.8808 (t) cc_final: 0.8250 (p) REVERT: A 121 PHE cc_start: 0.7718 (t80) cc_final: 0.7367 (t80) REVERT: A 161 PHE cc_start: 0.8114 (m-10) cc_final: 0.6904 (m-10) REVERT: A 194 LEU cc_start: 0.8460 (tp) cc_final: 0.8159 (mm) REVERT: A 211 ILE cc_start: 0.9014 (tt) cc_final: 0.8743 (tp) REVERT: A 230 GLN cc_start: 0.8818 (mt0) cc_final: 0.8296 (tp-100) REVERT: A 235 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8307 (mm-40) REVERT: A 237 LYS cc_start: 0.9040 (tmmt) cc_final: 0.8780 (pttm) REVERT: A 251 LEU cc_start: 0.8033 (mt) cc_final: 0.7014 (mm) REVERT: A 252 SER cc_start: 0.8215 (p) cc_final: 0.7670 (m) REVERT: A 255 TYR cc_start: 0.8033 (m-10) cc_final: 0.7640 (m-10) REVERT: A 262 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 272 PHE cc_start: 0.8199 (t80) cc_final: 0.7788 (t80) REVERT: A 276 LEU cc_start: 0.8718 (pp) cc_final: 0.8411 (pp) REVERT: A 279 ILE cc_start: 0.9111 (mm) cc_final: 0.8768 (tp) REVERT: A 282 CYS cc_start: 0.8811 (t) cc_final: 0.8408 (p) REVERT: A 283 MET cc_start: 0.7753 (mmp) cc_final: 0.7418 (mmp) REVERT: A 285 VAL cc_start: 0.8697 (m) cc_final: 0.8380 (p) REVERT: A 286 LYS cc_start: 0.8924 (tppt) cc_final: 0.8677 (tppt) REVERT: A 289 ASN cc_start: 0.8890 (m-40) cc_final: 0.8279 (m110) REVERT: A 293 LYS cc_start: 0.8358 (tppt) cc_final: 0.7861 (tppt) REVERT: A 305 ILE cc_start: 0.8673 (tp) cc_final: 0.8473 (tp) REVERT: A 309 ILE cc_start: 0.8928 (tp) cc_final: 0.8668 (pt) REVERT: A 321 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8118 (ttpp) REVERT: A 324 ASN cc_start: 0.8334 (t0) cc_final: 0.7995 (t0) REVERT: A 345 LEU cc_start: 0.8480 (mt) cc_final: 0.7658 (mt) REVERT: A 346 PHE cc_start: 0.8056 (m-10) cc_final: 0.7785 (m-10) REVERT: A 349 MET cc_start: 0.7275 (mtm) cc_final: 0.6863 (mtm) REVERT: A 353 SER cc_start: 0.8948 (m) cc_final: 0.8685 (p) REVERT: A 369 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8137 (mmtt) REVERT: A 371 TYR cc_start: 0.8353 (m-80) cc_final: 0.7764 (m-80) REVERT: A 385 PHE cc_start: 0.8148 (t80) cc_final: 0.7357 (t80) REVERT: A 392 ASN cc_start: 0.9267 (m-40) cc_final: 0.8930 (m-40) REVERT: A 394 PHE cc_start: 0.8328 (t80) cc_final: 0.7694 (t80) REVERT: A 397 PHE cc_start: 0.7904 (t80) cc_final: 0.7678 (t80) REVERT: A 432 MET cc_start: 0.8161 (tpt) cc_final: 0.7829 (tpt) REVERT: A 443 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 454 VAL cc_start: 0.9047 (t) cc_final: 0.8797 (t) REVERT: A 458 LEU cc_start: 0.8815 (mt) cc_final: 0.8518 (mt) REVERT: A 459 LYS cc_start: 0.8400 (tppp) cc_final: 0.6472 (tppp) REVERT: A 461 MET cc_start: 0.8941 (mtm) cc_final: 0.8697 (ptm) REVERT: A 463 MET cc_start: 0.8005 (mmp) cc_final: 0.7061 (mmp) REVERT: A 467 ASP cc_start: 0.7994 (p0) cc_final: 0.7752 (p0) REVERT: A 470 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7656 (ptt-90) REVERT: A 473 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8417 (mtpt) REVERT: A 476 LYS cc_start: 0.8815 (mttm) cc_final: 0.8470 (mmtm) REVERT: A 478 ASP cc_start: 0.8283 (m-30) cc_final: 0.8018 (m-30) REVERT: A 486 CYS cc_start: 0.8818 (t) cc_final: 0.8279 (p) REVERT: A 487 ILE cc_start: 0.8951 (mt) cc_final: 0.8596 (pt) REVERT: A 496 LEU cc_start: 0.8977 (tp) cc_final: 0.8667 (tp) REVERT: A 514 GLN cc_start: 0.8365 (tt0) cc_final: 0.7807 (tm-30) REVERT: A 530 TYR cc_start: 0.8182 (m-10) cc_final: 0.7834 (m-80) REVERT: A 546 LYS cc_start: 0.8518 (tptm) cc_final: 0.7940 (tptm) REVERT: A 549 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7199 (tpp-160) REVERT: A 560 ASP cc_start: 0.8459 (m-30) cc_final: 0.7962 (m-30) REVERT: A 563 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8177 (mmmt) REVERT: A 564 LYS cc_start: 0.8901 (tppt) cc_final: 0.8404 (tppt) REVERT: A 583 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8641 (ptmm) REVERT: A 677 ARG cc_start: 0.8362 (ttt180) cc_final: 0.7898 (tpp80) REVERT: A 678 MET cc_start: 0.8054 (mmm) cc_final: 0.7677 (mmm) REVERT: A 687 ASP cc_start: 0.8527 (t0) cc_final: 0.8120 (t0) REVERT: A 697 ASP cc_start: 0.8551 (m-30) cc_final: 0.7710 (p0) REVERT: A 701 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 705 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7574 (tp-100) REVERT: A 715 LYS cc_start: 0.8419 (mttm) cc_final: 0.7964 (mttm) REVERT: A 724 ASP cc_start: 0.8467 (m-30) cc_final: 0.7937 (m-30) REVERT: A 727 LEU cc_start: 0.8915 (mm) cc_final: 0.8334 (mt) REVERT: A 728 HIS cc_start: 0.8879 (t70) cc_final: 0.8590 (t70) REVERT: A 731 ASN cc_start: 0.8644 (m110) cc_final: 0.8315 (m110) REVERT: B 27 TYR cc_start: 0.8767 (m-10) cc_final: 0.8116 (m-10) REVERT: B 30 LEU cc_start: 0.8405 (pt) cc_final: 0.8202 (pt) REVERT: B 33 GLN cc_start: 0.8328 (pp30) cc_final: 0.8065 (pp30) REVERT: B 36 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8236 (mmm-85) REVERT: B 39 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7948 (mtt-85) REVERT: B 105 TYR cc_start: 0.7398 (m-80) cc_final: 0.7097 (m-80) REVERT: B 122 PHE cc_start: 0.8314 (m-80) cc_final: 0.7785 (m-80) REVERT: B 124 ILE cc_start: 0.8764 (mm) cc_final: 0.8322 (pt) REVERT: B 125 LEU cc_start: 0.8752 (mt) cc_final: 0.8457 (mt) REVERT: B 137 SER cc_start: 0.8072 (t) cc_final: 0.7768 (t) REVERT: B 144 VAL cc_start: 0.8656 (p) cc_final: 0.8173 (m) REVERT: B 147 MET cc_start: 0.9048 (mtt) cc_final: 0.8655 (mtt) REVERT: B 186 VAL cc_start: 0.9115 (p) cc_final: 0.8828 (m) REVERT: B 199 ILE cc_start: 0.8542 (tp) cc_final: 0.8307 (tp) REVERT: B 207 GLN cc_start: 0.8791 (tt0) cc_final: 0.8488 (tm-30) REVERT: B 213 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7170 (mtp180) REVERT: B 235 GLN cc_start: 0.8308 (pp30) cc_final: 0.7924 (pp30) REVERT: B 236 LEU cc_start: 0.8746 (tp) cc_final: 0.8239 (mt) REVERT: B 237 LYS cc_start: 0.9002 (pttt) cc_final: 0.8489 (pttp) REVERT: B 238 ILE cc_start: 0.8719 (tp) cc_final: 0.8516 (tp) REVERT: B 250 ILE cc_start: 0.8704 (pt) cc_final: 0.8421 (tp) REVERT: B 251 LEU cc_start: 0.8600 (mm) cc_final: 0.6575 (mm) REVERT: B 255 TYR cc_start: 0.7619 (m-10) cc_final: 0.6979 (m-80) REVERT: B 259 GLU cc_start: 0.8724 (tt0) cc_final: 0.8429 (tt0) REVERT: B 279 ILE cc_start: 0.8708 (pt) cc_final: 0.8071 (pt) REVERT: B 286 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8751 (mtmm) REVERT: B 290 ASP cc_start: 0.8441 (m-30) cc_final: 0.8198 (m-30) REVERT: B 303 GLU cc_start: 0.8981 (mp0) cc_final: 0.8623 (mp0) REVERT: B 319 LEU cc_start: 0.8710 (mt) cc_final: 0.8332 (pp) REVERT: B 321 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8104 (ttpp) REVERT: B 323 TYR cc_start: 0.8201 (m-80) cc_final: 0.7925 (m-80) REVERT: B 440 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7881 (mmm160) REVERT: B 443 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6889 (tm-30) REVERT: B 447 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8465 (ptpp) REVERT: B 455 ILE cc_start: 0.8737 (mt) cc_final: 0.8119 (mp) REVERT: B 459 LYS cc_start: 0.8668 (mmtt) cc_final: 0.7457 (mmtt) REVERT: B 463 MET cc_start: 0.7299 (mmm) cc_final: 0.6423 (mmm) REVERT: B 473 LYS cc_start: 0.8503 (mttp) cc_final: 0.7647 (pttm) REVERT: B 476 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8138 (mtpp) REVERT: B 477 THR cc_start: 0.8139 (m) cc_final: 0.7780 (p) REVERT: B 478 ASP cc_start: 0.8455 (p0) cc_final: 0.8164 (p0) REVERT: B 482 TRP cc_start: 0.8363 (t60) cc_final: 0.8093 (t60) REVERT: B 484 PHE cc_start: 0.8426 (t80) cc_final: 0.7866 (t80) REVERT: B 488 MET cc_start: 0.7812 (tpp) cc_final: 0.6486 (tpp) REVERT: B 491 ILE cc_start: 0.8921 (mt) cc_final: 0.8533 (mm) REVERT: B 492 LEU cc_start: 0.8650 (mt) cc_final: 0.7231 (mt) REVERT: B 494 LEU cc_start: 0.9173 (mt) cc_final: 0.8780 (mm) REVERT: B 496 LEU cc_start: 0.7969 (mt) cc_final: 0.7647 (mm) REVERT: B 512 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8256 (mtm-85) REVERT: B 514 GLN cc_start: 0.8871 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 537 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7737 (mtmm) REVERT: B 549 ARG cc_start: 0.8336 (ttt90) cc_final: 0.8057 (ttt90) REVERT: B 563 LYS cc_start: 0.9056 (tppt) cc_final: 0.8163 (tppt) REVERT: B 586 ARG cc_start: 0.8169 (ppt170) cc_final: 0.7953 (ttp80) REVERT: B 674 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8113 (ttm110) REVERT: B 677 ARG cc_start: 0.8619 (ttt180) cc_final: 0.7970 (ttm-80) REVERT: B 678 MET cc_start: 0.8217 (mmm) cc_final: 0.7812 (mmm) REVERT: B 682 GLU cc_start: 0.8323 (tp30) cc_final: 0.7326 (tp30) REVERT: B 701 GLU cc_start: 0.7847 (mp0) cc_final: 0.7641 (mp0) REVERT: B 702 LYS cc_start: 0.7686 (tptp) cc_final: 0.7106 (tptp) REVERT: B 705 GLN cc_start: 0.8723 (tt0) cc_final: 0.8439 (pp30) REVERT: B 716 ASP cc_start: 0.8262 (p0) cc_final: 0.7371 (t0) REVERT: B 719 PHE cc_start: 0.7905 (m-80) cc_final: 0.7590 (m-10) REVERT: B 720 LEU cc_start: 0.9152 (mp) cc_final: 0.8890 (mp) REVERT: B 727 LEU cc_start: 0.8980 (mt) cc_final: 0.7622 (mt) REVERT: B 730 GLN cc_start: 0.8965 (tt0) cc_final: 0.8434 (pp30) REVERT: B 731 ASN cc_start: 0.8512 (p0) cc_final: 0.7687 (p0) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3036 time to fit residues: 140.4719 Evaluate side-chains 331 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 0.0070 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091549 restraints weight = 26129.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094985 restraints weight = 15684.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097484 restraints weight = 10694.144| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5019 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= 0.193 Angle : 0.635 9.512 14128 Z= 0.325 Chirality : 0.044 0.312 1716 Planarity : 0.005 0.095 1757 Dihedral : 4.070 21.952 1415 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1319 helix: 0.45 (0.18), residues: 844 sheet: -1.83 (1.01), residues: 35 loop : -2.39 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 518 HIS 0.002 0.000 HIS A 723 PHE 0.026 0.001 PHE A 115 TYR 0.022 0.001 TYR B 578 ARG 0.018 0.001 ARG A 440 *********************** 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 353 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8454 (t80) cc_final: 0.8060 (t80) REVERT: A 38 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7588 (ttm110) REVERT: A 66 LYS cc_start: 0.8923 (tppt) cc_final: 0.8674 (tppt) REVERT: A 96 LEU cc_start: 0.8636 (mt) cc_final: 0.8304 (mm) REVERT: A 103 MET cc_start: 0.8526 (mtm) cc_final: 0.7797 (mtm) REVERT: A 105 TYR cc_start: 0.8527 (m-80) cc_final: 0.8111 (m-80) REVERT: A 118 TYR cc_start: 0.8392 (m-80) cc_final: 0.7988 (m-80) REVERT: A 119 SER cc_start: 0.8760 (t) cc_final: 0.8231 (p) REVERT: A 121 PHE cc_start: 0.7625 (t80) cc_final: 0.7245 (t80) REVERT: A 161 PHE cc_start: 0.8069 (m-10) cc_final: 0.6510 (m-10) REVERT: A 181 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.6850 (tpp-160) REVERT: A 194 LEU cc_start: 0.8445 (tp) cc_final: 0.8125 (mm) REVERT: A 211 ILE cc_start: 0.9020 (tt) cc_final: 0.8768 (tp) REVERT: A 230 GLN cc_start: 0.8778 (mt0) cc_final: 0.8249 (tp-100) REVERT: A 235 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8266 (mm-40) REVERT: A 237 LYS cc_start: 0.9027 (tmmt) cc_final: 0.8754 (pttm) REVERT: A 240 LEU cc_start: 0.8549 (mm) cc_final: 0.8333 (mp) REVERT: A 251 LEU cc_start: 0.8021 (mt) cc_final: 0.6998 (mm) REVERT: A 252 SER cc_start: 0.8216 (p) cc_final: 0.7705 (m) REVERT: A 255 TYR cc_start: 0.8016 (m-10) cc_final: 0.7610 (m-10) REVERT: A 262 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 272 PHE cc_start: 0.8146 (t80) cc_final: 0.7748 (t80) REVERT: A 276 LEU cc_start: 0.8736 (pp) cc_final: 0.8480 (pp) REVERT: A 279 ILE cc_start: 0.9090 (mm) cc_final: 0.8661 (tp) REVERT: A 282 CYS cc_start: 0.8768 (t) cc_final: 0.8389 (p) REVERT: A 283 MET cc_start: 0.7663 (mmp) cc_final: 0.7309 (mmp) REVERT: A 285 VAL cc_start: 0.8686 (m) cc_final: 0.8366 (p) REVERT: A 286 LYS cc_start: 0.8891 (tppt) cc_final: 0.8635 (tppt) REVERT: A 289 ASN cc_start: 0.8898 (m-40) cc_final: 0.8257 (m110) REVERT: A 293 LYS cc_start: 0.8334 (tppt) cc_final: 0.7862 (tppt) REVERT: A 305 ILE cc_start: 0.8663 (tp) cc_final: 0.8460 (tp) REVERT: A 309 ILE cc_start: 0.8928 (tp) cc_final: 0.8674 (pt) REVERT: A 321 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8115 (ttpp) REVERT: A 324 ASN cc_start: 0.8262 (t0) cc_final: 0.7939 (t0) REVERT: A 345 LEU cc_start: 0.8486 (mt) cc_final: 0.7654 (mt) REVERT: A 349 MET cc_start: 0.7207 (mtm) cc_final: 0.6802 (mtm) REVERT: A 353 SER cc_start: 0.8984 (m) cc_final: 0.8522 (p) REVERT: A 369 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8150 (mmtt) REVERT: A 371 TYR cc_start: 0.8363 (m-80) cc_final: 0.7818 (m-80) REVERT: A 385 PHE cc_start: 0.8172 (t80) cc_final: 0.7365 (t80) REVERT: A 392 ASN cc_start: 0.9277 (m-40) cc_final: 0.8941 (m-40) REVERT: A 394 PHE cc_start: 0.8308 (t80) cc_final: 0.7695 (t80) REVERT: A 397 PHE cc_start: 0.7917 (t80) cc_final: 0.7664 (t80) REVERT: A 432 MET cc_start: 0.8326 (tpt) cc_final: 0.7914 (tpt) REVERT: A 443 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 454 VAL cc_start: 0.9078 (t) cc_final: 0.8805 (t) REVERT: A 458 LEU cc_start: 0.8721 (mt) cc_final: 0.8467 (mt) REVERT: A 459 LYS cc_start: 0.8412 (tppp) cc_final: 0.6544 (tppp) REVERT: A 461 MET cc_start: 0.8900 (mtm) cc_final: 0.8601 (ptp) REVERT: A 463 MET cc_start: 0.8003 (mmp) cc_final: 0.7031 (mmp) REVERT: A 467 ASP cc_start: 0.7960 (p0) cc_final: 0.7677 (p0) REVERT: A 470 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7281 (ptt-90) REVERT: A 473 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8586 (pttp) REVERT: A 476 LYS cc_start: 0.8820 (mttm) cc_final: 0.8490 (mmtm) REVERT: A 478 ASP cc_start: 0.8275 (m-30) cc_final: 0.7994 (m-30) REVERT: A 486 CYS cc_start: 0.8820 (t) cc_final: 0.8282 (p) REVERT: A 487 ILE cc_start: 0.8949 (mt) cc_final: 0.8596 (pt) REVERT: A 496 LEU cc_start: 0.8979 (tp) cc_final: 0.8682 (tp) REVERT: A 514 GLN cc_start: 0.8317 (tt0) cc_final: 0.7788 (tm-30) REVERT: A 530 TYR cc_start: 0.8198 (m-10) cc_final: 0.7892 (m-80) REVERT: A 531 LYS cc_start: 0.8261 (mmpt) cc_final: 0.8059 (mmpt) REVERT: A 546 LYS cc_start: 0.8542 (tptm) cc_final: 0.7959 (tptm) REVERT: A 549 ARG cc_start: 0.7861 (ttt90) cc_final: 0.7049 (tpp-160) REVERT: A 560 ASP cc_start: 0.8453 (m-30) cc_final: 0.7952 (m-30) REVERT: A 563 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8192 (mmmt) REVERT: A 564 LYS cc_start: 0.8912 (tppt) cc_final: 0.8463 (tppt) REVERT: A 677 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7913 (tpp80) REVERT: A 678 MET cc_start: 0.8085 (mmm) cc_final: 0.7771 (mmm) REVERT: A 687 ASP cc_start: 0.8531 (t0) cc_final: 0.8102 (t0) REVERT: A 697 ASP cc_start: 0.8563 (m-30) cc_final: 0.7707 (p0) REVERT: A 701 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 705 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7539 (tp-100) REVERT: A 723 HIS cc_start: 0.8026 (t70) cc_final: 0.7811 (t70) REVERT: A 724 ASP cc_start: 0.8397 (m-30) cc_final: 0.7840 (m-30) REVERT: A 727 LEU cc_start: 0.8914 (mm) cc_final: 0.8309 (mt) REVERT: A 728 HIS cc_start: 0.8876 (t70) cc_final: 0.8587 (t70) REVERT: A 731 ASN cc_start: 0.8595 (m110) cc_final: 0.8269 (m110) REVERT: B 27 TYR cc_start: 0.8796 (m-10) cc_final: 0.8179 (m-10) REVERT: B 33 GLN cc_start: 0.8306 (pp30) cc_final: 0.7990 (pp30) REVERT: B 105 TYR cc_start: 0.7321 (m-80) cc_final: 0.7033 (m-80) REVERT: B 122 PHE cc_start: 0.8326 (m-80) cc_final: 0.7784 (m-80) REVERT: B 124 ILE cc_start: 0.8818 (mm) cc_final: 0.8393 (pt) REVERT: B 125 LEU cc_start: 0.8769 (mt) cc_final: 0.8474 (mt) REVERT: B 137 SER cc_start: 0.8047 (t) cc_final: 0.7768 (t) REVERT: B 144 VAL cc_start: 0.8568 (p) cc_final: 0.8124 (m) REVERT: B 147 MET cc_start: 0.9072 (mtt) cc_final: 0.8683 (mtt) REVERT: B 186 VAL cc_start: 0.9024 (p) cc_final: 0.8727 (m) REVERT: B 196 VAL cc_start: 0.8957 (t) cc_final: 0.8661 (t) REVERT: B 199 ILE cc_start: 0.8525 (tp) cc_final: 0.8234 (tp) REVERT: B 207 GLN cc_start: 0.8803 (tt0) cc_final: 0.8416 (tm-30) REVERT: B 213 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7151 (mtp180) REVERT: B 230 GLN cc_start: 0.8425 (pp30) cc_final: 0.7930 (pp30) REVERT: B 235 GLN cc_start: 0.8276 (pp30) cc_final: 0.7951 (pp30) REVERT: B 236 LEU cc_start: 0.8746 (tp) cc_final: 0.8229 (mt) REVERT: B 237 LYS cc_start: 0.8978 (pttt) cc_final: 0.8482 (pttp) REVERT: B 238 ILE cc_start: 0.8701 (tp) cc_final: 0.8475 (tp) REVERT: B 250 ILE cc_start: 0.8690 (pt) cc_final: 0.8428 (tp) REVERT: B 251 LEU cc_start: 0.8600 (mm) cc_final: 0.6593 (mm) REVERT: B 255 TYR cc_start: 0.7646 (m-10) cc_final: 0.6999 (m-80) REVERT: B 259 GLU cc_start: 0.8743 (tt0) cc_final: 0.8427 (tt0) REVERT: B 279 ILE cc_start: 0.8690 (pt) cc_final: 0.8149 (pt) REVERT: B 286 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8791 (mtmm) REVERT: B 290 ASP cc_start: 0.8409 (m-30) cc_final: 0.8169 (m-30) REVERT: B 303 GLU cc_start: 0.8986 (mp0) cc_final: 0.8616 (mp0) REVERT: B 319 LEU cc_start: 0.8697 (mt) cc_final: 0.8348 (pp) REVERT: B 321 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8137 (ttpp) REVERT: B 323 TYR cc_start: 0.8246 (m-80) cc_final: 0.7938 (m-80) REVERT: B 440 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7966 (ttp80) REVERT: B 447 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8464 (ptpp) REVERT: B 463 MET cc_start: 0.7337 (mmm) cc_final: 0.6446 (mmm) REVERT: B 473 LYS cc_start: 0.8434 (mttp) cc_final: 0.7652 (pttt) REVERT: B 476 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8294 (mmmt) REVERT: B 477 THR cc_start: 0.8110 (m) cc_final: 0.7718 (p) REVERT: B 478 ASP cc_start: 0.8457 (p0) cc_final: 0.8218 (p0) REVERT: B 484 PHE cc_start: 0.8402 (t80) cc_final: 0.7849 (t80) REVERT: B 488 MET cc_start: 0.7731 (tpp) cc_final: 0.6455 (tpp) REVERT: B 491 ILE cc_start: 0.8918 (mt) cc_final: 0.8529 (mm) REVERT: B 492 LEU cc_start: 0.8678 (mt) cc_final: 0.7279 (mt) REVERT: B 496 LEU cc_start: 0.7939 (mt) cc_final: 0.7618 (mm) REVERT: B 512 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8274 (mtm-85) REVERT: B 514 GLN cc_start: 0.8844 (tt0) cc_final: 0.8411 (tm-30) REVERT: B 537 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7767 (mtmm) REVERT: B 549 ARG cc_start: 0.8296 (ttt90) cc_final: 0.7780 (ptm160) REVERT: B 563 LYS cc_start: 0.9008 (tppt) cc_final: 0.8149 (tppt) REVERT: B 666 SER cc_start: 0.8760 (p) cc_final: 0.8525 (p) REVERT: B 674 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8077 (ttm110) REVERT: B 677 ARG cc_start: 0.8616 (ttt180) cc_final: 0.7906 (ttm-80) REVERT: B 678 MET cc_start: 0.8180 (mmm) cc_final: 0.7822 (mmm) REVERT: B 691 TYR cc_start: 0.7669 (m-80) cc_final: 0.6968 (m-80) REVERT: B 701 GLU cc_start: 0.7895 (mp0) cc_final: 0.7682 (mp0) REVERT: B 702 LYS cc_start: 0.7862 (tptp) cc_final: 0.7099 (tptp) REVERT: B 705 GLN cc_start: 0.8619 (tt0) cc_final: 0.8348 (pp30) REVERT: B 716 ASP cc_start: 0.8289 (p0) cc_final: 0.8019 (p0) REVERT: B 719 PHE cc_start: 0.7930 (m-80) cc_final: 0.7694 (m-10) REVERT: B 720 LEU cc_start: 0.9165 (mp) cc_final: 0.8915 (mp) REVERT: B 727 LEU cc_start: 0.8973 (mt) cc_final: 0.7599 (mt) REVERT: B 730 GLN cc_start: 0.8953 (tt0) cc_final: 0.8436 (pp30) REVERT: B 731 ASN cc_start: 0.8471 (p0) cc_final: 0.7529 (p0) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2858 time to fit residues: 131.3122 Evaluate side-chains 340 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 81 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN A 567 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.114789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092390 restraints weight = 26134.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095824 restraints weight = 15958.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098285 restraints weight = 10892.916| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5137 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= 0.173 Angle : 0.627 9.734 14128 Z= 0.319 Chirality : 0.044 0.322 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.039 22.134 1415 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1319 helix: 0.56 (0.18), residues: 824 sheet: -1.70 (1.01), residues: 34 loop : -2.14 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 518 HIS 0.003 0.000 HIS A 723 PHE 0.018 0.001 PHE B 385 TYR 0.017 0.001 TYR B 578 ARG 0.014 0.001 ARG A 440 *********************** 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 362 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.132 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: symmetry clash REVERT: A 20 TYR cc_start: 0.8427 (t80) cc_final: 0.8137 (t80) REVERT: A 38 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7612 (ttm110) REVERT: A 66 LYS cc_start: 0.8902 (tppt) cc_final: 0.8610 (tppt) REVERT: A 96 LEU cc_start: 0.8700 (mt) cc_final: 0.8409 (mm) REVERT: A 99 THR cc_start: 0.8932 (t) cc_final: 0.8222 (t) REVERT: A 105 TYR cc_start: 0.8311 (m-80) cc_final: 0.7886 (m-80) REVERT: A 118 TYR cc_start: 0.8363 (m-80) cc_final: 0.7896 (m-80) REVERT: A 119 SER cc_start: 0.8759 (t) cc_final: 0.8242 (p) REVERT: A 121 PHE cc_start: 0.7502 (t80) cc_final: 0.7174 (t80) REVERT: A 181 ARG cc_start: 0.7507 (tpp-160) cc_final: 0.7222 (tpp80) REVERT: A 211 ILE cc_start: 0.8996 (tt) cc_final: 0.8736 (tp) REVERT: A 230 GLN cc_start: 0.8810 (mt0) cc_final: 0.8260 (tp-100) REVERT: A 235 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8315 (mm-40) REVERT: A 237 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8758 (pttm) REVERT: A 240 LEU cc_start: 0.8539 (mm) cc_final: 0.8327 (mp) REVERT: A 251 LEU cc_start: 0.7957 (mt) cc_final: 0.6936 (mm) REVERT: A 252 SER cc_start: 0.8226 (p) cc_final: 0.7681 (m) REVERT: A 255 TYR cc_start: 0.8012 (m-10) cc_final: 0.7606 (m-10) REVERT: A 262 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 272 PHE cc_start: 0.8170 (t80) cc_final: 0.7859 (t80) REVERT: A 276 LEU cc_start: 0.8716 (pp) cc_final: 0.8468 (pp) REVERT: A 279 ILE cc_start: 0.9091 (mm) cc_final: 0.8650 (tp) REVERT: A 282 CYS cc_start: 0.8778 (t) cc_final: 0.8278 (p) REVERT: A 283 MET cc_start: 0.7670 (mmp) cc_final: 0.7269 (mmp) REVERT: A 285 VAL cc_start: 0.8706 (m) cc_final: 0.8370 (p) REVERT: A 286 LYS cc_start: 0.8880 (tppt) cc_final: 0.8612 (tppt) REVERT: A 289 ASN cc_start: 0.8901 (m-40) cc_final: 0.8273 (m-40) REVERT: A 293 LYS cc_start: 0.8308 (tppt) cc_final: 0.7830 (tppt) REVERT: A 305 ILE cc_start: 0.8635 (tp) cc_final: 0.8400 (tp) REVERT: A 309 ILE cc_start: 0.8919 (tp) cc_final: 0.8657 (pt) REVERT: A 321 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8145 (ttpp) REVERT: A 322 ASN cc_start: 0.8168 (m-40) cc_final: 0.7865 (m110) REVERT: A 324 ASN cc_start: 0.8214 (t0) cc_final: 0.7908 (t0) REVERT: A 345 LEU cc_start: 0.8455 (mt) cc_final: 0.7609 (mt) REVERT: A 349 MET cc_start: 0.7208 (mtm) cc_final: 0.6877 (mtm) REVERT: A 353 SER cc_start: 0.8928 (m) cc_final: 0.8665 (p) REVERT: A 371 TYR cc_start: 0.8325 (m-80) cc_final: 0.7799 (m-80) REVERT: A 385 PHE cc_start: 0.8027 (t80) cc_final: 0.7434 (t80) REVERT: A 392 ASN cc_start: 0.9254 (m-40) cc_final: 0.8897 (m-40) REVERT: A 394 PHE cc_start: 0.8308 (t80) cc_final: 0.7665 (t80) REVERT: A 432 MET cc_start: 0.8295 (tpt) cc_final: 0.7896 (tpt) REVERT: A 443 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 454 VAL cc_start: 0.9098 (t) cc_final: 0.8814 (t) REVERT: A 458 LEU cc_start: 0.8824 (mt) cc_final: 0.8537 (mt) REVERT: A 459 LYS cc_start: 0.8429 (tppp) cc_final: 0.6612 (tppp) REVERT: A 461 MET cc_start: 0.8906 (mtm) cc_final: 0.8663 (ptp) REVERT: A 463 MET cc_start: 0.8000 (mmp) cc_final: 0.7248 (mmp) REVERT: A 467 ASP cc_start: 0.7955 (p0) cc_final: 0.7647 (p0) REVERT: A 470 ARG cc_start: 0.7882 (ptp-170) cc_final: 0.7624 (ptt-90) REVERT: A 473 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8378 (mtpt) REVERT: A 476 LYS cc_start: 0.8811 (mttm) cc_final: 0.8496 (mmtm) REVERT: A 478 ASP cc_start: 0.8257 (m-30) cc_final: 0.7995 (m-30) REVERT: A 486 CYS cc_start: 0.8767 (t) cc_final: 0.8238 (p) REVERT: A 487 ILE cc_start: 0.8920 (mt) cc_final: 0.8562 (pt) REVERT: A 496 LEU cc_start: 0.8965 (tp) cc_final: 0.8660 (tp) REVERT: A 514 GLN cc_start: 0.8322 (tt0) cc_final: 0.7814 (tm-30) REVERT: A 530 TYR cc_start: 0.8158 (m-10) cc_final: 0.7889 (m-80) REVERT: A 549 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7251 (tpp-160) REVERT: A 560 ASP cc_start: 0.8458 (m-30) cc_final: 0.8149 (m-30) REVERT: A 563 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8276 (mmmt) REVERT: A 564 LYS cc_start: 0.8945 (tppt) cc_final: 0.8402 (tppt) REVERT: A 677 ARG cc_start: 0.8399 (ttt180) cc_final: 0.7898 (tpp80) REVERT: A 678 MET cc_start: 0.8066 (mmm) cc_final: 0.7674 (mmm) REVERT: A 687 ASP cc_start: 0.8461 (t0) cc_final: 0.8045 (t0) REVERT: A 697 ASP cc_start: 0.8574 (m-30) cc_final: 0.7671 (p0) REVERT: A 701 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 705 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7490 (tp-100) REVERT: A 715 LYS cc_start: 0.8262 (mttm) cc_final: 0.7926 (mttm) REVERT: A 723 HIS cc_start: 0.7946 (t70) cc_final: 0.7662 (t70) REVERT: A 724 ASP cc_start: 0.8375 (m-30) cc_final: 0.7807 (m-30) REVERT: A 727 LEU cc_start: 0.8899 (mm) cc_final: 0.8413 (mm) REVERT: A 728 HIS cc_start: 0.8848 (t70) cc_final: 0.8613 (t70) REVERT: A 731 ASN cc_start: 0.8578 (m110) cc_final: 0.8244 (m110) REVERT: B 27 TYR cc_start: 0.8805 (m-10) cc_final: 0.8167 (m-10) REVERT: B 33 GLN cc_start: 0.8325 (pp30) cc_final: 0.8016 (pp30) REVERT: B 36 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8187 (mmm-85) REVERT: B 105 TYR cc_start: 0.7265 (m-80) cc_final: 0.6952 (m-80) REVERT: B 122 PHE cc_start: 0.8333 (m-80) cc_final: 0.7771 (m-80) REVERT: B 124 ILE cc_start: 0.8789 (mm) cc_final: 0.8360 (pt) REVERT: B 125 LEU cc_start: 0.8753 (mt) cc_final: 0.8469 (mt) REVERT: B 137 SER cc_start: 0.8057 (t) cc_final: 0.7751 (t) REVERT: B 144 VAL cc_start: 0.8598 (p) cc_final: 0.8167 (m) REVERT: B 147 MET cc_start: 0.9017 (mtt) cc_final: 0.8651 (mtt) REVERT: B 186 VAL cc_start: 0.9013 (p) cc_final: 0.8712 (m) REVERT: B 199 ILE cc_start: 0.8465 (tp) cc_final: 0.8212 (tp) REVERT: B 207 GLN cc_start: 0.8807 (tt0) cc_final: 0.8378 (tm-30) REVERT: B 230 GLN cc_start: 0.8377 (pp30) cc_final: 0.7921 (pp30) REVERT: B 235 GLN cc_start: 0.8311 (pp30) cc_final: 0.7954 (pp30) REVERT: B 236 LEU cc_start: 0.8723 (tp) cc_final: 0.8250 (mt) REVERT: B 237 LYS cc_start: 0.8932 (pttt) cc_final: 0.8407 (pttp) REVERT: B 238 ILE cc_start: 0.8740 (tp) cc_final: 0.8360 (pt) REVERT: B 250 ILE cc_start: 0.8656 (pt) cc_final: 0.8425 (tp) REVERT: B 251 LEU cc_start: 0.8568 (mm) cc_final: 0.6626 (mm) REVERT: B 255 TYR cc_start: 0.7617 (m-10) cc_final: 0.6974 (m-80) REVERT: B 259 GLU cc_start: 0.8713 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 260 ILE cc_start: 0.9220 (mm) cc_final: 0.8881 (mt) REVERT: B 279 ILE cc_start: 0.8670 (pt) cc_final: 0.8101 (pt) REVERT: B 286 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8748 (mtmm) REVERT: B 303 GLU cc_start: 0.8993 (mp0) cc_final: 0.8603 (mp0) REVERT: B 318 ASN cc_start: 0.8579 (t0) cc_final: 0.7793 (t0) REVERT: B 319 LEU cc_start: 0.8715 (mt) cc_final: 0.8344 (mt) REVERT: B 321 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8267 (ttpp) REVERT: B 322 ASN cc_start: 0.8203 (m-40) cc_final: 0.7746 (t0) REVERT: B 323 TYR cc_start: 0.8246 (m-80) cc_final: 0.7038 (m-80) REVERT: B 440 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7859 (mmm160) REVERT: B 443 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 447 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8462 (ptpp) REVERT: B 463 MET cc_start: 0.7346 (mmm) cc_final: 0.6433 (mmm) REVERT: B 473 LYS cc_start: 0.8430 (mttp) cc_final: 0.7488 (mtmm) REVERT: B 477 THR cc_start: 0.8099 (m) cc_final: 0.7703 (p) REVERT: B 478 ASP cc_start: 0.8443 (p0) cc_final: 0.8178 (p0) REVERT: B 484 PHE cc_start: 0.8395 (t80) cc_final: 0.7833 (t80) REVERT: B 488 MET cc_start: 0.7702 (tpp) cc_final: 0.6503 (tpp) REVERT: B 491 ILE cc_start: 0.8927 (mt) cc_final: 0.8509 (mm) REVERT: B 492 LEU cc_start: 0.8679 (mt) cc_final: 0.7292 (mt) REVERT: B 494 LEU cc_start: 0.9177 (mt) cc_final: 0.8875 (mm) REVERT: B 495 ASP cc_start: 0.7524 (p0) cc_final: 0.6977 (p0) REVERT: B 496 LEU cc_start: 0.7999 (mt) cc_final: 0.7196 (mt) REVERT: B 512 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8150 (mtm-85) REVERT: B 514 GLN cc_start: 0.8845 (tt0) cc_final: 0.8431 (tm-30) REVERT: B 537 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7767 (mtmm) REVERT: B 549 ARG cc_start: 0.8298 (ttt90) cc_final: 0.7976 (ttt90) REVERT: B 563 LYS cc_start: 0.9028 (tppt) cc_final: 0.7874 (tppt) REVERT: B 565 CYS cc_start: 0.8755 (t) cc_final: 0.8513 (p) REVERT: B 567 ASN cc_start: 0.8480 (m-40) cc_final: 0.7852 (m110) REVERT: B 580 LYS cc_start: 0.8741 (tttp) cc_final: 0.8155 (tmtt) REVERT: B 674 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8037 (ttm110) REVERT: B 677 ARG cc_start: 0.8589 (ttt180) cc_final: 0.7870 (ttm-80) REVERT: B 678 MET cc_start: 0.8206 (mmm) cc_final: 0.7808 (mmm) REVERT: B 685 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8010 (ttt-90) REVERT: B 691 TYR cc_start: 0.7611 (m-80) cc_final: 0.6977 (m-80) REVERT: B 694 LEU cc_start: 0.8346 (pt) cc_final: 0.8082 (pp) REVERT: B 702 LYS cc_start: 0.7874 (tptp) cc_final: 0.7332 (tptp) REVERT: B 705 GLN cc_start: 0.8595 (tt0) cc_final: 0.8351 (pp30) REVERT: B 716 ASP cc_start: 0.8260 (p0) cc_final: 0.7367 (t0) REVERT: B 720 LEU cc_start: 0.9156 (mp) cc_final: 0.8874 (mp) REVERT: B 727 LEU cc_start: 0.8966 (mt) cc_final: 0.7598 (mt) REVERT: B 730 GLN cc_start: 0.8955 (tt0) cc_final: 0.8392 (pp30) REVERT: B 731 ASN cc_start: 0.8471 (p0) cc_final: 0.7654 (p0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2827 time to fit residues: 133.7043 Evaluate side-chains 341 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093252 restraints weight = 26097.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096801 restraints weight = 15589.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099319 restraints weight = 10523.519| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5234 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= 0.177 Angle : 0.633 9.640 14128 Z= 0.322 Chirality : 0.044 0.317 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.073 21.593 1415 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1319 helix: 0.57 (0.18), residues: 827 sheet: -1.90 (0.99), residues: 34 loop : -2.20 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 518 HIS 0.006 0.000 HIS A 723 PHE 0.019 0.001 PHE B 385 TYR 0.030 0.001 TYR B 578 ARG 0.010 0.001 ARG A 440 ********************** 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 350 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.038 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: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8465 (t80) cc_final: 0.8158 (t80) REVERT: A 29 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 38 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7616 (ttm110) REVERT: A 66 LYS cc_start: 0.8911 (tppt) cc_final: 0.8617 (tppt) REVERT: A 96 LEU cc_start: 0.8657 (mt) cc_final: 0.8353 (mm) REVERT: A 119 SER cc_start: 0.8767 (t) cc_final: 0.8252 (p) REVERT: A 121 PHE cc_start: 0.7502 (t80) cc_final: 0.7130 (t80) REVERT: A 181 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7177 (tpp80) REVERT: A 194 LEU cc_start: 0.8433 (tp) cc_final: 0.8104 (mm) REVERT: A 211 ILE cc_start: 0.8988 (tt) cc_final: 0.8751 (tp) REVERT: A 230 GLN cc_start: 0.8833 (mt0) cc_final: 0.8259 (tp-100) REVERT: A 235 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8317 (mm-40) REVERT: A 237 LYS cc_start: 0.9027 (tmmt) cc_final: 0.8719 (pttm) REVERT: A 240 LEU cc_start: 0.8500 (mm) cc_final: 0.8274 (mp) REVERT: A 251 LEU cc_start: 0.7958 (mt) cc_final: 0.6939 (mm) REVERT: A 252 SER cc_start: 0.8217 (p) cc_final: 0.7675 (m) REVERT: A 255 TYR cc_start: 0.7996 (m-10) cc_final: 0.7574 (m-10) REVERT: A 262 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 272 PHE cc_start: 0.8209 (t80) cc_final: 0.7834 (t80) REVERT: A 276 LEU cc_start: 0.8700 (pp) cc_final: 0.8403 (pp) REVERT: A 279 ILE cc_start: 0.9072 (mm) cc_final: 0.8761 (mm) REVERT: A 282 CYS cc_start: 0.8780 (t) cc_final: 0.8302 (p) REVERT: A 283 MET cc_start: 0.7654 (mmp) cc_final: 0.7347 (mmp) REVERT: A 285 VAL cc_start: 0.8705 (m) cc_final: 0.8380 (p) REVERT: A 286 LYS cc_start: 0.8896 (tppt) cc_final: 0.8634 (tppt) REVERT: A 289 ASN cc_start: 0.8912 (m-40) cc_final: 0.8291 (m-40) REVERT: A 293 LYS cc_start: 0.8314 (tppt) cc_final: 0.7832 (tppt) REVERT: A 305 ILE cc_start: 0.8639 (tp) cc_final: 0.8431 (tp) REVERT: A 309 ILE cc_start: 0.8939 (tp) cc_final: 0.8668 (pt) REVERT: A 321 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8148 (ttpp) REVERT: A 322 ASN cc_start: 0.8195 (m-40) cc_final: 0.7951 (m110) REVERT: A 324 ASN cc_start: 0.8288 (t0) cc_final: 0.7999 (t0) REVERT: A 345 LEU cc_start: 0.8396 (mt) cc_final: 0.7518 (mt) REVERT: A 346 PHE cc_start: 0.8018 (m-10) cc_final: 0.7745 (m-10) REVERT: A 349 MET cc_start: 0.7210 (mtm) cc_final: 0.6818 (mtm) REVERT: A 353 SER cc_start: 0.9002 (m) cc_final: 0.8759 (p) REVERT: A 371 TYR cc_start: 0.8321 (m-80) cc_final: 0.7754 (m-80) REVERT: A 385 PHE cc_start: 0.8045 (t80) cc_final: 0.7432 (t80) REVERT: A 392 ASN cc_start: 0.9277 (m-40) cc_final: 0.8922 (m-40) REVERT: A 394 PHE cc_start: 0.8279 (t80) cc_final: 0.7688 (t80) REVERT: A 397 PHE cc_start: 0.7909 (t80) cc_final: 0.7381 (t80) REVERT: A 414 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 432 MET cc_start: 0.8207 (tpt) cc_final: 0.7842 (tpt) REVERT: A 443 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 454 VAL cc_start: 0.9112 (t) cc_final: 0.8851 (t) REVERT: A 459 LYS cc_start: 0.8413 (tppp) cc_final: 0.6682 (tppp) REVERT: A 461 MET cc_start: 0.8911 (mtm) cc_final: 0.8626 (ptp) REVERT: A 463 MET cc_start: 0.8011 (mmp) cc_final: 0.7213 (mmp) REVERT: A 467 ASP cc_start: 0.7987 (p0) cc_final: 0.7687 (p0) REVERT: A 470 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7600 (ptt-90) REVERT: A 473 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8397 (mtpt) REVERT: A 476 LYS cc_start: 0.8805 (mttm) cc_final: 0.8490 (mmtm) REVERT: A 478 ASP cc_start: 0.8315 (m-30) cc_final: 0.8047 (m-30) REVERT: A 486 CYS cc_start: 0.8805 (t) cc_final: 0.8248 (p) REVERT: A 487 ILE cc_start: 0.8925 (mt) cc_final: 0.8542 (pt) REVERT: A 496 LEU cc_start: 0.8962 (tp) cc_final: 0.8408 (tp) REVERT: A 503 LEU cc_start: 0.9254 (mt) cc_final: 0.9015 (mm) REVERT: A 514 GLN cc_start: 0.8308 (tt0) cc_final: 0.7779 (tm-30) REVERT: A 549 ARG cc_start: 0.7779 (ttt90) cc_final: 0.7067 (tpp-160) REVERT: A 560 ASP cc_start: 0.8452 (m-30) cc_final: 0.8152 (m-30) REVERT: A 563 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8192 (mmmt) REVERT: A 564 LYS cc_start: 0.8921 (tppt) cc_final: 0.8448 (tppt) REVERT: A 677 ARG cc_start: 0.8406 (ttt180) cc_final: 0.7895 (tpp80) REVERT: A 678 MET cc_start: 0.8026 (mmm) cc_final: 0.7628 (mmm) REVERT: A 687 ASP cc_start: 0.8437 (t0) cc_final: 0.8034 (t0) REVERT: A 697 ASP cc_start: 0.8524 (m-30) cc_final: 0.7703 (p0) REVERT: A 701 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 705 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7459 (tp-100) REVERT: A 715 LYS cc_start: 0.8282 (mttm) cc_final: 0.7824 (mttm) REVERT: A 724 ASP cc_start: 0.8334 (m-30) cc_final: 0.7758 (m-30) REVERT: A 727 LEU cc_start: 0.8794 (mm) cc_final: 0.8313 (mm) REVERT: A 728 HIS cc_start: 0.8862 (t70) cc_final: 0.8469 (t-90) REVERT: A 731 ASN cc_start: 0.8523 (m110) cc_final: 0.8209 (m110) REVERT: B 27 TYR cc_start: 0.8798 (m-10) cc_final: 0.8147 (m-10) REVERT: B 33 GLN cc_start: 0.8281 (pp30) cc_final: 0.7968 (pp30) REVERT: B 105 TYR cc_start: 0.7252 (m-80) cc_final: 0.6924 (m-80) REVERT: B 122 PHE cc_start: 0.8336 (m-80) cc_final: 0.7778 (m-80) REVERT: B 124 ILE cc_start: 0.8785 (mm) cc_final: 0.8356 (pt) REVERT: B 125 LEU cc_start: 0.8761 (mt) cc_final: 0.8471 (mt) REVERT: B 137 SER cc_start: 0.8055 (t) cc_final: 0.7763 (t) REVERT: B 144 VAL cc_start: 0.8586 (p) cc_final: 0.8156 (m) REVERT: B 147 MET cc_start: 0.9066 (mtt) cc_final: 0.8672 (mtt) REVERT: B 186 VAL cc_start: 0.9012 (p) cc_final: 0.8706 (m) REVERT: B 199 ILE cc_start: 0.8527 (tp) cc_final: 0.8281 (tp) REVERT: B 207 GLN cc_start: 0.8800 (tt0) cc_final: 0.8357 (tm-30) REVERT: B 230 GLN cc_start: 0.8416 (pp30) cc_final: 0.7951 (pp30) REVERT: B 235 GLN cc_start: 0.8339 (pp30) cc_final: 0.8040 (pp30) REVERT: B 236 LEU cc_start: 0.8749 (tp) cc_final: 0.8299 (mt) REVERT: B 237 LYS cc_start: 0.8948 (pttt) cc_final: 0.8397 (pttp) REVERT: B 238 ILE cc_start: 0.8699 (tp) cc_final: 0.8304 (pt) REVERT: B 250 ILE cc_start: 0.8662 (pt) cc_final: 0.8320 (mm) REVERT: B 251 LEU cc_start: 0.8574 (mm) cc_final: 0.6657 (mm) REVERT: B 255 TYR cc_start: 0.7642 (m-10) cc_final: 0.7069 (m-80) REVERT: B 259 GLU cc_start: 0.8705 (tt0) cc_final: 0.8404 (tt0) REVERT: B 279 ILE cc_start: 0.8625 (pt) cc_final: 0.8034 (pt) REVERT: B 286 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8815 (mtmm) REVERT: B 303 GLU cc_start: 0.8983 (mp0) cc_final: 0.8592 (mp0) REVERT: B 319 LEU cc_start: 0.8728 (mt) cc_final: 0.8417 (mt) REVERT: B 321 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8106 (ttpp) REVERT: B 323 TYR cc_start: 0.8240 (m-80) cc_final: 0.7894 (m-80) REVERT: B 440 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8004 (ptm-80) REVERT: B 447 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8490 (ptpp) REVERT: B 463 MET cc_start: 0.7371 (mmm) cc_final: 0.6450 (mmm) REVERT: B 473 LYS cc_start: 0.8435 (mttp) cc_final: 0.7609 (pttm) REVERT: B 476 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8295 (mmmt) REVERT: B 477 THR cc_start: 0.8102 (m) cc_final: 0.7715 (p) REVERT: B 478 ASP cc_start: 0.8506 (p0) cc_final: 0.8213 (p0) REVERT: B 484 PHE cc_start: 0.8405 (t80) cc_final: 0.7841 (t80) REVERT: B 488 MET cc_start: 0.7759 (tpp) cc_final: 0.6531 (tpp) REVERT: B 491 ILE cc_start: 0.8915 (mt) cc_final: 0.8620 (mm) REVERT: B 492 LEU cc_start: 0.8689 (mt) cc_final: 0.7324 (mt) REVERT: B 494 LEU cc_start: 0.9205 (mt) cc_final: 0.8952 (mm) REVERT: B 496 LEU cc_start: 0.7968 (mt) cc_final: 0.7615 (mm) REVERT: B 512 ARG cc_start: 0.8582 (mtm180) cc_final: 0.8125 (mtm-85) REVERT: B 514 GLN cc_start: 0.8852 (tt0) cc_final: 0.8431 (tm-30) REVERT: B 537 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7755 (mtmm) REVERT: B 549 ARG cc_start: 0.8334 (ttt90) cc_final: 0.8072 (ttt-90) REVERT: B 563 LYS cc_start: 0.9017 (tppt) cc_final: 0.8114 (tppt) REVERT: B 674 ARG cc_start: 0.8889 (ttm110) cc_final: 0.8067 (ttm110) REVERT: B 677 ARG cc_start: 0.8546 (ttt180) cc_final: 0.7947 (ttm-80) REVERT: B 678 MET cc_start: 0.8169 (mmm) cc_final: 0.7816 (mmm) REVERT: B 685 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7495 (ttt-90) REVERT: B 694 LEU cc_start: 0.8346 (pt) cc_final: 0.8098 (pp) REVERT: B 702 LYS cc_start: 0.7985 (tptp) cc_final: 0.7214 (tptp) REVERT: B 705 GLN cc_start: 0.8556 (tt0) cc_final: 0.8326 (pp30) REVERT: B 716 ASP cc_start: 0.8210 (p0) cc_final: 0.7444 (t0) REVERT: B 720 LEU cc_start: 0.9160 (mp) cc_final: 0.8856 (mp) REVERT: B 727 LEU cc_start: 0.8907 (mt) cc_final: 0.7541 (mt) REVERT: B 730 GLN cc_start: 0.8906 (tt0) cc_final: 0.8400 (pp30) REVERT: B 731 ASN cc_start: 0.8449 (p0) cc_final: 0.7530 (p0) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2796 time to fit residues: 128.0298 Evaluate side-chains 336 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 131 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.115243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093116 restraints weight = 26001.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096616 restraints weight = 15826.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099027 restraints weight = 10705.288| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5289 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= 0.175 Angle : 0.642 10.705 14128 Z= 0.325 Chirality : 0.044 0.316 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.053 21.506 1415 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1319 helix: 0.59 (0.18), residues: 826 sheet: -1.68 (1.04), residues: 34 loop : -2.14 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 518 HIS 0.003 0.000 HIS A 723 PHE 0.023 0.001 PHE B 719 TYR 0.025 0.001 TYR B 578 ARG 0.009 0.001 ARG B 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.57 seconds wall clock time: 67 minutes 55.91 seconds (4075.91 seconds total)