Starting phenix.real_space_refine on Mon Jun 9 04:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlb_32580/06_2025/7wlb_32580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlb_32580/06_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_32580/06_2025/7wlb_32580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlb_32580/06_2025/7wlb_32580.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlb_32580/06_2025/7wlb_32580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlb_32580/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.62, per 1000 atoms: 0.75 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 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: 1.07 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: 3.07 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3212 1.35 - 1.46: 2296 1.46 - 1.58: 4823 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10395 Sorted by residual: bond pdb=" C THR B 224 " pdb=" N THR B 225 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.13e+00 bond pdb=" CA VAL A 111 " pdb=" CB VAL A 111 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.97e-01 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.85e-01 bond pdb=" C GLU B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.79e-01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 13733 1.11 - 2.21: 303 2.21 - 3.32: 63 3.32 - 4.43: 19 4.43 - 5.53: 10 Bond angle restraints: 14128 Sorted by residual: angle pdb=" N ARG A 134 " pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 114.56 111.35 3.21 1.27e+00 6.20e-01 6.38e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.31e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.65 -4.31 2.08e+00 2.31e-01 4.29e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 125.64 -3.67 1.80e+00 3.09e-01 4.15e+00 angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 121.97 125.59 -3.62 1.80e+00 3.09e-01 4.04e+00 ... (remaining 14123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 5960 16.92 - 33.83: 175 33.83 - 50.75: 40 50.75 - 67.67: 1 67.67 - 84.59: 4 Dihedral angle restraints: 6180 sinusoidal: 2353 harmonic: 3827 Sorted by residual: dihedral pdb=" CA LEU B 695 " pdb=" C LEU B 695 " pdb=" N GLN B 696 " pdb=" CA GLN B 696 " ideal model delta harmonic sigma weight residual -180.00 -164.38 -15.62 0 5.00e+00 4.00e-02 9.76e+00 dihedral pdb=" CB GLU B 259 " pdb=" CG GLU B 259 " pdb=" CD GLU B 259 " pdb=" OE1 GLU B 259 " ideal model delta sinusoidal sigma weight residual 0.00 84.59 -84.59 1 3.00e+01 1.11e-03 9.66e+00 dihedral pdb=" N ARG B 43 " pdb=" CA ARG B 43 " pdb=" CB ARG B 43 " pdb=" CG ARG B 43 " ideal model delta sinusoidal sigma weight residual -180.00 -128.33 -51.67 3 1.50e+01 4.44e-03 9.04e+00 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 963 0.026 - 0.051: 491 0.051 - 0.077: 179 0.077 - 0.103: 67 0.103 - 0.128: 16 Chirality restraints: 1716 Sorted by residual: chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1713 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 76 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.020 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO B 654 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.017 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1026 2.74 - 3.28: 10986 3.28 - 3.82: 16738 3.82 - 4.36: 19313 4.36 - 4.90: 32636 Nonbonded interactions: 80699 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.284 3.040 ... (remaining 80694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10395 Z= 0.091 Angle : 0.445 5.533 14128 Z= 0.253 Chirality : 0.037 0.128 1716 Planarity : 0.003 0.042 1757 Dihedral : 8.675 84.585 3714 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.92 % Allowed : 5.70 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.24025 ( 546) hydrogen bonds : angle 6.82005 ( 1596) covalent geometry : bond 0.00168 (10395) covalent geometry : angle 0.44474 (14128) *********************** 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 : 1.018 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: 0.2831 time to fit residues: 160.6872 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 : 1.138 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095573 restraints weight = 25990.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.099065 restraints weight = 15465.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101533 restraints weight = 10403.780| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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= 0.188 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 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 546) hydrogen bonds : angle 4.19171 ( 1596) covalent geometry : bond 0.00376 (10395) covalent geometry : angle 0.64203 (14128) *********************** 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 : 1.039 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: 0.7918 (mtp-110) cc_final: 0.7661 (ttm110) REVERT: A 66 LYS cc_start: 0.8788 (tppt) cc_final: 0.8577 (tppt) REVERT: A 96 LEU cc_start: 0.8922 (mt) cc_final: 0.8567 (pp) REVERT: A 100 LEU cc_start: 0.8850 (mm) cc_final: 0.8543 (mm) REVERT: A 105 TYR cc_start: 0.8563 (m-80) cc_final: 0.8330 (m-80) REVERT: A 119 SER cc_start: 0.8777 (t) cc_final: 0.8142 (p) REVERT: A 198 ILE cc_start: 0.8567 (mt) cc_final: 0.8358 (tp) REVERT: A 211 ILE cc_start: 0.8816 (tt) cc_final: 0.8571 (tp) REVERT: A 230 GLN cc_start: 0.8925 (mt0) cc_final: 0.8402 (tp-100) REVERT: A 235 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8026 (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: 0.6978 (mm) REVERT: A 252 SER cc_start: 0.8076 (p) cc_final: 0.7528 (m) REVERT: A 255 TYR cc_start: 0.8018 (m-10) cc_final: 0.7624 (m-10) REVERT: A 263 ASN cc_start: 0.8941 (t0) cc_final: 0.8641 (t0) REVERT: A 276 LEU cc_start: 0.8745 (pp) cc_final: 0.8521 (pp) REVERT: A 282 CYS cc_start: 0.8780 (t) cc_final: 0.8306 (p) REVERT: A 283 MET cc_start: 0.7891 (mmp) cc_final: 0.7656 (mmp) REVERT: A 286 LYS cc_start: 0.9135 (tppt) cc_final: 0.8651 (tppt) REVERT: A 293 LYS cc_start: 0.8083 (tppt) cc_final: 0.7753 (tppt) REVERT: A 303 GLU cc_start: 0.8619 (pm20) cc_final: 0.8403 (pm20) REVERT: A 305 ILE cc_start: 0.8676 (tp) cc_final: 0.8393 (tp) REVERT: A 306 VAL cc_start: 0.8991 (p) cc_final: 0.8656 (m) REVERT: A 309 ILE cc_start: 0.8866 (tp) cc_final: 0.8581 (pt) REVERT: A 321 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8087 (ptmm) REVERT: A 324 ASN cc_start: 0.8183 (t0) cc_final: 0.7707 (t0) REVERT: A 349 MET cc_start: 0.7287 (mtm) cc_final: 0.6917 (mtm) REVERT: A 354 PHE cc_start: 0.8830 (t80) cc_final: 0.8598 (t80) REVERT: A 369 LYS cc_start: 0.8743 (mmtt) cc_final: 0.7928 (mmtt) REVERT: A 371 TYR cc_start: 0.8391 (m-80) cc_final: 0.7786 (m-80) REVERT: A 382 ASN cc_start: 0.8942 (m110) cc_final: 0.8705 (m110) REVERT: A 384 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 385 PHE cc_start: 0.8283 (t80) cc_final: 0.7448 (t80) REVERT: A 394 PHE cc_start: 0.8316 (t80) cc_final: 0.7570 (t80) REVERT: A 401 PHE cc_start: 0.7866 (p90) cc_final: 0.7543 (p90) REVERT: A 414 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 432 MET cc_start: 0.8202 (tpt) cc_final: 0.7868 (tpt) REVERT: A 438 LEU cc_start: 0.8761 (tt) cc_final: 0.8517 (tt) REVERT: A 443 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 454 VAL cc_start: 0.9022 (t) cc_final: 0.8080 (t) REVERT: A 458 LEU cc_start: 0.8750 (mt) cc_final: 0.8451 (mt) REVERT: A 459 LYS cc_start: 0.8486 (tppp) cc_final: 0.6473 (tppp) REVERT: A 463 MET cc_start: 0.7924 (mmp) cc_final: 0.6568 (mmp) REVERT: A 473 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8411 (mtpt) REVERT: A 476 LYS cc_start: 0.8884 (mttm) cc_final: 0.8578 (mttt) REVERT: A 478 ASP cc_start: 0.8217 (m-30) cc_final: 0.8005 (m-30) REVERT: A 486 CYS cc_start: 0.8743 (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: 0.8400 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 530 TYR cc_start: 0.8367 (m-10) cc_final: 0.7995 (m-10) REVERT: A 535 HIS cc_start: 0.7309 (m90) cc_final: 0.7017 (m-70) REVERT: A 537 LYS cc_start: 0.8638 (tttt) cc_final: 0.8135 (tttt) REVERT: A 549 ARG cc_start: 0.7752 (ttt90) cc_final: 0.6849 (ttm-80) REVERT: A 560 ASP cc_start: 0.8296 (m-30) cc_final: 0.8053 (m-30) REVERT: A 563 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8246 (mmmt) REVERT: A 564 LYS cc_start: 0.8844 (tppt) cc_final: 0.8400 (tppt) REVERT: A 681 LYS cc_start: 0.8077 (tptt) cc_final: 0.7689 (tptt) REVERT: A 687 ASP cc_start: 0.8450 (t0) cc_final: 0.8082 (t0) REVERT: A 701 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 704 GLU cc_start: 0.7445 (tt0) cc_final: 0.7165 (tt0) REVERT: A 705 GLN cc_start: 0.8028 (mm110) cc_final: 0.6864 (mm-40) REVERT: A 715 LYS cc_start: 0.8625 (mttm) cc_final: 0.8205 (ttmm) REVERT: A 724 ASP cc_start: 0.8488 (m-30) cc_final: 0.8016 (m-30) REVERT: A 727 LEU cc_start: 0.9092 (mm) cc_final: 0.8109 (mt) REVERT: A 728 HIS cc_start: 0.8868 (t70) cc_final: 0.8516 (t70) REVERT: A 731 ASN cc_start: 0.8378 (m110) cc_final: 0.8066 (m110) REVERT: B 27 TYR cc_start: 0.8648 (m-10) cc_final: 0.7834 (m-10) REVERT: B 37 GLU cc_start: 0.8053 (pp20) cc_final: 0.7582 (pp20) REVERT: B 122 PHE cc_start: 0.8086 (m-80) cc_final: 0.7574 (m-80) REVERT: B 124 ILE cc_start: 0.8652 (mm) cc_final: 0.8262 (pt) REVERT: B 125 LEU cc_start: 0.8707 (mt) cc_final: 0.8390 (mt) REVERT: B 144 VAL cc_start: 0.8676 (p) cc_final: 0.8339 (m) REVERT: B 147 MET cc_start: 0.8946 (mtt) cc_final: 0.8638 (mtt) REVERT: B 213 ARG cc_start: 0.7569 (mtp85) cc_final: 0.6901 (mtp85) REVERT: B 230 GLN cc_start: 0.8414 (tp40) cc_final: 0.7791 (tp40) REVERT: B 233 VAL cc_start: 0.9108 (p) cc_final: 0.8887 (m) REVERT: B 237 LYS cc_start: 0.8902 (pttt) cc_final: 0.8422 (pttp) REVERT: B 238 ILE cc_start: 0.8723 (tp) cc_final: 0.8247 (pt) REVERT: B 245 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8182 (mtmm) REVERT: B 250 ILE cc_start: 0.8611 (pt) cc_final: 0.8385 (tp) REVERT: B 251 LEU cc_start: 0.8545 (mm) cc_final: 0.6645 (mm) REVERT: B 254 ILE cc_start: 0.8576 (mm) cc_final: 0.7958 (tp) REVERT: B 255 TYR cc_start: 0.7563 (m-10) cc_final: 0.6861 (m-80) REVERT: B 286 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8873 (mttt) REVERT: B 319 LEU cc_start: 0.8676 (mt) cc_final: 0.8142 (pp) REVERT: B 323 TYR cc_start: 0.8087 (m-80) cc_final: 0.7810 (m-80) REVERT: B 356 ILE cc_start: 0.8255 (mt) cc_final: 0.7953 (mp) REVERT: B 440 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7907 (mtt-85) REVERT: B 446 GLN cc_start: 0.8318 (tt0) cc_final: 0.7912 (tt0) REVERT: B 455 ILE cc_start: 0.8650 (mt) cc_final: 0.7740 (mp) REVERT: B 459 LYS cc_start: 0.8713 (mmtt) cc_final: 0.7664 (mmtt) REVERT: B 463 MET cc_start: 0.7110 (mmm) cc_final: 0.6207 (mmm) REVERT: B 477 THR cc_start: 0.8361 (m) cc_final: 0.8063 (p) REVERT: B 482 TRP cc_start: 0.8315 (t60) cc_final: 0.8095 (t60) REVERT: B 484 PHE cc_start: 0.8550 (t80) cc_final: 0.7949 (t80) REVERT: B 488 MET cc_start: 0.7731 (tpp) cc_final: 0.6558 (tpp) REVERT: B 491 ILE cc_start: 0.8880 (mt) cc_final: 0.8501 (mm) REVERT: B 492 LEU cc_start: 0.8744 (mt) cc_final: 0.7442 (mt) REVERT: B 494 LEU cc_start: 0.9078 (mt) cc_final: 0.8722 (mm) REVERT: B 495 ASP cc_start: 0.7469 (p0) cc_final: 0.6866 (p0) REVERT: B 496 LEU cc_start: 0.8015 (mt) cc_final: 0.7204 (mt) REVERT: B 512 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8242 (mtm-85) REVERT: B 514 GLN cc_start: 0.8930 (tt0) cc_final: 0.8461 (tm-30) REVERT: B 535 HIS cc_start: 0.7743 (m-70) cc_final: 0.7349 (m-70) REVERT: B 537 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7640 (mtmm) REVERT: B 563 LYS cc_start: 0.9028 (tppt) cc_final: 0.8202 (tppt) REVERT: B 580 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8318 (mmmt) REVERT: B 590 LYS cc_start: 0.8444 (pttm) cc_final: 0.7922 (pttm) REVERT: B 655 ILE cc_start: 0.8885 (mt) cc_final: 0.8673 (tt) REVERT: B 666 SER cc_start: 0.8731 (p) cc_final: 0.8464 (p) REVERT: B 673 VAL cc_start: 0.9058 (t) cc_final: 0.8711 (t) REVERT: B 674 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8221 (ttm110) REVERT: B 677 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8168 (mtp85) REVERT: B 678 MET cc_start: 0.8120 (mmm) cc_final: 0.7741 (mmm) REVERT: B 682 GLU cc_start: 0.8454 (tp30) cc_final: 0.8003 (tp30) REVERT: B 684 GLN cc_start: 0.9175 (tp40) cc_final: 0.8814 (tp40) REVERT: B 702 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7565 (tptp) REVERT: B 705 GLN cc_start: 0.8429 (tt0) cc_final: 0.8166 (tt0) REVERT: B 716 ASP cc_start: 0.8109 (t0) cc_final: 0.7901 (p0) REVERT: B 720 LEU cc_start: 0.8983 (mp) cc_final: 0.8689 (mt) REVERT: B 727 LEU cc_start: 0.8930 (mt) cc_final: 0.8651 (mt) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2758 time to fit residues: 135.4689 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 : 1.021 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 0.0470 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 207 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** 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 = 0.3796 r_free = 0.3796 target = 0.116124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093554 restraints weight = 26138.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097038 restraints weight = 15804.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099492 restraints weight = 10698.157| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3698 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= 0.160 Angle : 0.603 11.066 14128 Z= 0.312 Chirality : 0.042 0.237 1716 Planarity : 0.005 0.107 1757 Dihedral : 3.752 22.339 1415 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -1.55 (0.22), residues: 1319 helix: -0.01 (0.18), residues: 824 sheet: -2.20 (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 535 PHE 0.027 0.001 PHE A 115 TYR 0.017 0.001 TYR A 27 ARG 0.018 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 546) hydrogen bonds : angle 3.97973 ( 1596) covalent geometry : bond 0.00329 (10395) covalent geometry : angle 0.60313 (14128) *********************** 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 380 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.001 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 96 LEU cc_start: 0.8896 (mt) cc_final: 0.8602 (mm) REVERT: A 103 MET cc_start: 0.8364 (mtm) cc_final: 0.7655 (mtm) REVERT: A 105 TYR cc_start: 0.8674 (m-80) cc_final: 0.8122 (m-80) REVERT: A 119 SER cc_start: 0.8751 (t) cc_final: 0.8091 (p) REVERT: A 121 PHE cc_start: 0.7710 (t80) cc_final: 0.7460 (t80) REVERT: A 211 ILE cc_start: 0.8910 (tt) cc_final: 0.8627 (tp) REVERT: A 230 GLN cc_start: 0.8889 (mt0) cc_final: 0.8210 (mt0) REVERT: A 237 LYS cc_start: 0.8940 (pttp) cc_final: 0.8610 (pttp) REVERT: A 251 LEU cc_start: 0.8035 (mt) cc_final: 0.6998 (mm) REVERT: A 252 SER cc_start: 0.8143 (p) cc_final: 0.7607 (m) REVERT: A 255 TYR cc_start: 0.8042 (m-10) cc_final: 0.7638 (m-10) REVERT: A 259 GLU cc_start: 0.8457 (tt0) cc_final: 0.8250 (tt0) REVERT: A 262 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 272 PHE cc_start: 0.8128 (t80) cc_final: 0.7748 (t80) REVERT: A 276 LEU cc_start: 0.8756 (pp) cc_final: 0.8480 (pp) REVERT: A 279 ILE cc_start: 0.9181 (mm) cc_final: 0.8734 (mm) REVERT: A 282 CYS cc_start: 0.8770 (t) cc_final: 0.8311 (p) REVERT: A 283 MET cc_start: 0.7815 (mmp) cc_final: 0.7548 (mmp) REVERT: A 286 LYS cc_start: 0.9148 (tppt) cc_final: 0.8600 (tppt) REVERT: A 293 LYS cc_start: 0.8133 (tppt) cc_final: 0.7761 (tppt) REVERT: A 305 ILE cc_start: 0.8675 (tp) cc_final: 0.8433 (tp) REVERT: A 306 VAL cc_start: 0.8926 (p) cc_final: 0.8535 (m) REVERT: A 309 ILE cc_start: 0.8902 (tp) cc_final: 0.8614 (pt) REVERT: A 315 TYR cc_start: 0.8088 (t80) cc_final: 0.7834 (t80) REVERT: A 321 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8126 (ptmm) REVERT: A 324 ASN cc_start: 0.8221 (t0) cc_final: 0.7715 (t0) REVERT: A 345 LEU cc_start: 0.8463 (mt) cc_final: 0.7662 (mp) REVERT: A 349 MET cc_start: 0.7304 (mtm) cc_final: 0.6928 (mtm) REVERT: A 353 SER cc_start: 0.9012 (m) cc_final: 0.8691 (p) REVERT: A 369 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8523 (tppt) REVERT: A 371 TYR cc_start: 0.8346 (m-80) cc_final: 0.7791 (m-80) REVERT: A 382 ASN cc_start: 0.8903 (m110) cc_final: 0.8637 (t0) REVERT: A 385 PHE cc_start: 0.8224 (t80) cc_final: 0.7322 (t80) REVERT: A 388 PHE cc_start: 0.8993 (m-80) cc_final: 0.8647 (m-80) REVERT: A 392 ASN cc_start: 0.9242 (m-40) cc_final: 0.8919 (m-40) REVERT: A 394 PHE cc_start: 0.8285 (t80) cc_final: 0.7585 (t80) REVERT: A 397 PHE cc_start: 0.7840 (t80) cc_final: 0.7605 (t80) REVERT: A 409 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7715 (ttm170) REVERT: A 432 MET cc_start: 0.8173 (tpt) cc_final: 0.7854 (tpt) REVERT: A 443 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 454 VAL cc_start: 0.9012 (t) cc_final: 0.8614 (t) REVERT: A 458 LEU cc_start: 0.8891 (mt) cc_final: 0.8588 (mt) REVERT: A 459 LYS cc_start: 0.8486 (tppp) cc_final: 0.6485 (tppp) REVERT: A 461 MET cc_start: 0.8883 (mtm) cc_final: 0.8683 (ptp) REVERT: A 462 PHE cc_start: 0.8475 (m-80) cc_final: 0.8074 (m-80) REVERT: A 463 MET cc_start: 0.7903 (mmp) cc_final: 0.6683 (mmp) REVERT: A 470 ARG cc_start: 0.7979 (ptp-170) cc_final: 0.7251 (ptt-90) REVERT: A 473 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8593 (pttp) REVERT: A 474 GLN cc_start: 0.7845 (mt0) cc_final: 0.7528 (mt0) REVERT: A 476 LYS cc_start: 0.8780 (mttm) cc_final: 0.8478 (mmtt) REVERT: A 478 ASP cc_start: 0.8230 (m-30) cc_final: 0.8021 (m-30) REVERT: A 486 CYS cc_start: 0.8800 (t) cc_final: 0.8270 (p) REVERT: A 487 ILE cc_start: 0.8961 (mt) cc_final: 0.8638 (pt) REVERT: A 488 MET cc_start: 0.7946 (mmp) cc_final: 0.7741 (mmp) REVERT: A 496 LEU cc_start: 0.8886 (tp) cc_final: 0.8628 (tp) REVERT: A 530 TYR cc_start: 0.8388 (m-10) cc_final: 0.8156 (m-10) REVERT: A 535 HIS cc_start: 0.7448 (m90) cc_final: 0.7128 (m170) REVERT: A 540 GLU cc_start: 0.7654 (pt0) cc_final: 0.6991 (pm20) REVERT: A 549 ARG cc_start: 0.7793 (ttt90) cc_final: 0.7410 (tpp80) REVERT: A 563 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8260 (mmmt) REVERT: A 564 LYS cc_start: 0.8888 (tppt) cc_final: 0.8424 (tppt) REVERT: A 580 LYS cc_start: 0.7985 (tttt) cc_final: 0.7155 (tttp) REVERT: A 677 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7777 (tpp80) REVERT: A 678 MET cc_start: 0.7949 (mmm) cc_final: 0.7688 (mmm) REVERT: A 687 ASP cc_start: 0.8536 (t0) cc_final: 0.8154 (t0) REVERT: A 691 TYR cc_start: 0.7388 (m-10) cc_final: 0.7148 (m-10) REVERT: A 696 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 697 ASP cc_start: 0.8626 (m-30) cc_final: 0.7799 (p0) REVERT: A 701 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 704 GLU cc_start: 0.7476 (tt0) cc_final: 0.7166 (tt0) REVERT: A 715 LYS cc_start: 0.8550 (mttm) cc_final: 0.8323 (mtpp) REVERT: A 723 HIS cc_start: 0.8302 (t70) cc_final: 0.8056 (t-90) REVERT: A 724 ASP cc_start: 0.8488 (m-30) cc_final: 0.8273 (m-30) REVERT: A 727 LEU cc_start: 0.8871 (mm) cc_final: 0.7977 (mt) REVERT: A 731 ASN cc_start: 0.8601 (m110) cc_final: 0.8055 (m-40) REVERT: B 27 TYR cc_start: 0.8690 (m-10) cc_final: 0.7949 (m-10) REVERT: B 37 GLU cc_start: 0.8113 (pp20) cc_final: 0.7880 (pp20) REVERT: B 39 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7988 (mtp180) REVERT: B 105 TYR cc_start: 0.7386 (m-80) cc_final: 0.6915 (m-80) REVERT: B 122 PHE cc_start: 0.8121 (m-80) cc_final: 0.7601 (m-80) REVERT: B 124 ILE cc_start: 0.8663 (mm) cc_final: 0.8250 (pt) REVERT: B 125 LEU cc_start: 0.8770 (mt) cc_final: 0.8433 (mt) REVERT: B 144 VAL cc_start: 0.8623 (p) cc_final: 0.8113 (m) REVERT: B 147 MET cc_start: 0.8978 (mtt) cc_final: 0.8668 (mtt) REVERT: B 199 ILE cc_start: 0.8509 (tp) cc_final: 0.8305 (tp) REVERT: B 207 GLN cc_start: 0.8712 (tt0) cc_final: 0.8490 (tm-30) REVERT: B 213 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7359 (mtm180) REVERT: B 230 GLN cc_start: 0.8388 (tp40) cc_final: 0.7897 (tp40) REVERT: B 233 VAL cc_start: 0.9122 (p) cc_final: 0.8751 (m) REVERT: B 236 LEU cc_start: 0.8832 (tp) cc_final: 0.7995 (mt) REVERT: B 237 LYS cc_start: 0.9052 (pttt) cc_final: 0.8278 (pttp) REVERT: B 238 ILE cc_start: 0.8650 (tp) cc_final: 0.8262 (pt) REVERT: B 241 ASN cc_start: 0.8037 (m110) cc_final: 0.7520 (m-40) REVERT: B 250 ILE cc_start: 0.8679 (pt) cc_final: 0.8361 (tp) REVERT: B 251 LEU cc_start: 0.8639 (mm) cc_final: 0.6530 (mm) REVERT: B 254 ILE cc_start: 0.8530 (mm) cc_final: 0.7998 (tp) REVERT: B 255 TYR cc_start: 0.7484 (m-10) cc_final: 0.6773 (m-80) REVERT: B 259 GLU cc_start: 0.8708 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 260 ILE cc_start: 0.9187 (mm) cc_final: 0.8908 (mt) REVERT: B 280 ILE cc_start: 0.8414 (mm) cc_final: 0.8184 (mm) REVERT: B 283 MET cc_start: 0.8063 (ptp) cc_final: 0.7639 (ptp) REVERT: B 303 GLU cc_start: 0.8946 (mp0) cc_final: 0.8678 (mp0) REVERT: B 319 LEU cc_start: 0.8655 (mt) cc_final: 0.8329 (mt) REVERT: B 322 ASN cc_start: 0.7977 (m-40) cc_final: 0.7752 (m-40) REVERT: B 323 TYR cc_start: 0.8107 (m-80) cc_final: 0.7819 (m-80) REVERT: B 356 ILE cc_start: 0.8221 (mt) cc_final: 0.7931 (mp) REVERT: B 446 GLN cc_start: 0.8357 (tt0) cc_final: 0.8134 (tt0) REVERT: B 455 ILE cc_start: 0.8715 (mt) cc_final: 0.8253 (mp) REVERT: B 459 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7472 (mmtt) REVERT: B 463 MET cc_start: 0.7170 (mmm) cc_final: 0.6212 (mmm) REVERT: B 482 TRP cc_start: 0.8346 (t60) cc_final: 0.8085 (t60) REVERT: B 484 PHE cc_start: 0.8460 (t80) cc_final: 0.7888 (t80) REVERT: B 488 MET cc_start: 0.7719 (tpp) cc_final: 0.6508 (tpp) REVERT: B 491 ILE cc_start: 0.8950 (mt) cc_final: 0.8574 (mm) REVERT: B 492 LEU cc_start: 0.8706 (mt) cc_final: 0.7375 (mt) REVERT: B 494 LEU cc_start: 0.9129 (mt) cc_final: 0.8558 (tt) REVERT: B 495 ASP cc_start: 0.7413 (p0) cc_final: 0.7027 (p0) REVERT: B 496 LEU cc_start: 0.7926 (mt) cc_final: 0.7081 (mt) REVERT: B 512 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8204 (mtm-85) REVERT: B 514 GLN cc_start: 0.8872 (tt0) cc_final: 0.8401 (tm-30) REVERT: B 526 SER cc_start: 0.8882 (m) cc_final: 0.8673 (p) REVERT: B 535 HIS cc_start: 0.7701 (m90) cc_final: 0.7074 (m90) REVERT: B 537 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7737 (mtmt) REVERT: B 563 LYS cc_start: 0.9015 (tppt) cc_final: 0.7973 (tppt) REVERT: B 567 ASN cc_start: 0.8270 (m-40) cc_final: 0.7490 (m110) REVERT: B 577 VAL cc_start: 0.9018 (m) cc_final: 0.8772 (p) REVERT: B 578 TYR cc_start: 0.7934 (t80) cc_final: 0.6192 (t80) REVERT: B 580 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8250 (mmmt) REVERT: B 586 ARG cc_start: 0.8390 (ppt170) cc_final: 0.8175 (ttp80) REVERT: B 677 ARG cc_start: 0.8616 (ttt180) cc_final: 0.7998 (ttm-80) REVERT: B 678 MET cc_start: 0.8144 (mmm) cc_final: 0.7799 (mmm) REVERT: B 682 GLU cc_start: 0.8394 (tp30) cc_final: 0.7895 (tp30) REVERT: B 684 GLN cc_start: 0.9157 (tp40) cc_final: 0.8937 (tp-100) REVERT: B 685 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7606 (mtm180) REVERT: B 701 GLU cc_start: 0.7850 (mp0) cc_final: 0.7415 (mp0) REVERT: B 720 LEU cc_start: 0.9065 (mp) cc_final: 0.8677 (mt) REVERT: B 724 ASP cc_start: 0.8569 (m-30) cc_final: 0.8254 (m-30) REVERT: B 727 LEU cc_start: 0.8940 (mt) cc_final: 0.8659 (mt) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2686 time to fit residues: 134.0263 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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: 0.7980 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 207 GLN B 322 ASN B 464 GLN B 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.113515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091182 restraints weight = 25967.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094447 restraints weight = 15744.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096842 restraints weight = 10822.033| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10395 Z= 0.178 Angle : 0.623 9.390 14128 Z= 0.325 Chirality : 0.043 0.262 1716 Planarity : 0.004 0.044 1757 Dihedral : 3.926 22.663 1415 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -1.11 (0.23), residues: 1319 helix: 0.32 (0.18), residues: 823 sheet: -1.84 (1.00), residues: 34 loop : -2.62 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 74 HIS 0.005 0.001 HIS A 723 PHE 0.028 0.001 PHE A 115 TYR 0.024 0.002 TYR A 118 ARG 0.012 0.001 ARG B 674 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 546) hydrogen bonds : angle 3.92365 ( 1596) covalent geometry : bond 0.00360 (10395) covalent geometry : angle 0.62322 (14128) *********************** 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 360 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 1.000 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: 0.8485 (t80) cc_final: 0.7941 (t80) REVERT: A 66 LYS cc_start: 0.8946 (tptt) cc_final: 0.8674 (tptt) REVERT: A 96 LEU cc_start: 0.8833 (mt) cc_final: 0.8467 (mm) REVERT: A 103 MET cc_start: 0.8401 (mtm) cc_final: 0.7843 (mtm) REVERT: A 105 TYR cc_start: 0.8728 (m-80) cc_final: 0.8191 (m-80) REVERT: A 118 TYR cc_start: 0.8220 (m-80) cc_final: 0.7614 (m-80) REVERT: A 119 SER cc_start: 0.8751 (t) cc_final: 0.8204 (p) REVERT: A 121 PHE cc_start: 0.7794 (t80) cc_final: 0.7469 (t80) REVERT: A 181 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7326 (tpp80) REVERT: A 185 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8475 (tpp80) REVERT: A 211 ILE cc_start: 0.9030 (tt) cc_final: 0.8718 (tp) REVERT: A 230 GLN cc_start: 0.8927 (mt0) cc_final: 0.8388 (tp-100) REVERT: A 237 LYS cc_start: 0.8979 (pttp) cc_final: 0.8775 (pptt) REVERT: A 251 LEU cc_start: 0.8124 (mt) cc_final: 0.7918 (mm) REVERT: A 252 SER cc_start: 0.8216 (p) cc_final: 0.7737 (m) REVERT: A 262 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 272 PHE cc_start: 0.8125 (t80) cc_final: 0.7777 (t80) REVERT: A 276 LEU cc_start: 0.8779 (pp) cc_final: 0.8488 (pp) REVERT: A 279 ILE cc_start: 0.9128 (mm) cc_final: 0.8771 (tp) REVERT: A 282 CYS cc_start: 0.8764 (t) cc_final: 0.8328 (p) REVERT: A 283 MET cc_start: 0.7698 (mmp) cc_final: 0.7413 (mmp) REVERT: A 285 VAL cc_start: 0.8642 (m) cc_final: 0.8338 (p) REVERT: A 286 LYS cc_start: 0.9088 (tppt) cc_final: 0.8633 (tppt) REVERT: A 293 LYS cc_start: 0.8316 (tppt) cc_final: 0.7847 (tppt) REVERT: A 305 ILE cc_start: 0.8671 (tp) cc_final: 0.8299 (pt) REVERT: A 306 VAL cc_start: 0.8897 (p) cc_final: 0.8596 (m) REVERT: A 309 ILE cc_start: 0.8940 (tp) cc_final: 0.8675 (pt) REVERT: A 324 ASN cc_start: 0.8307 (t0) cc_final: 0.7917 (t0) REVERT: A 345 LEU cc_start: 0.8529 (mt) cc_final: 0.7680 (mp) REVERT: A 349 MET cc_start: 0.7316 (mtm) cc_final: 0.6943 (mtm) REVERT: A 353 SER cc_start: 0.8994 (m) cc_final: 0.8674 (p) REVERT: A 369 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8557 (tppt) REVERT: A 371 TYR cc_start: 0.8363 (m-80) cc_final: 0.7749 (m-80) REVERT: A 382 ASN cc_start: 0.8934 (m110) cc_final: 0.8730 (t0) REVERT: A 385 PHE cc_start: 0.8197 (t80) cc_final: 0.7402 (t80) REVERT: A 388 PHE cc_start: 0.8990 (m-80) cc_final: 0.8653 (m-80) REVERT: A 394 PHE cc_start: 0.8308 (t80) cc_final: 0.7728 (t80) REVERT: A 397 PHE cc_start: 0.7914 (t80) cc_final: 0.7597 (t80) REVERT: A 432 MET cc_start: 0.8267 (tpt) cc_final: 0.7919 (tpt) REVERT: A 443 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 454 VAL cc_start: 0.9018 (t) cc_final: 0.8643 (t) REVERT: A 458 LEU cc_start: 0.8810 (mt) cc_final: 0.8602 (mt) REVERT: A 459 LYS cc_start: 0.8453 (tppp) cc_final: 0.6609 (tppp) REVERT: A 463 MET cc_start: 0.7973 (mmp) cc_final: 0.6742 (mmp) REVERT: A 470 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.7438 (ptt-90) REVERT: A 473 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8590 (pttp) REVERT: A 476 LYS cc_start: 0.8766 (mttm) cc_final: 0.8448 (mmtt) REVERT: A 486 CYS cc_start: 0.8861 (t) cc_final: 0.8282 (p) REVERT: A 487 ILE cc_start: 0.8982 (mt) cc_final: 0.8671 (pt) REVERT: A 496 LEU cc_start: 0.8946 (tp) cc_final: 0.8653 (tp) REVERT: A 530 TYR cc_start: 0.8250 (m-10) cc_final: 0.7941 (m-80) REVERT: A 540 GLU cc_start: 0.7691 (pt0) cc_final: 0.7037 (pm20) REVERT: A 549 ARG cc_start: 0.7800 (ttt90) cc_final: 0.7078 (tpp-160) REVERT: A 560 ASP cc_start: 0.8504 (m-30) cc_final: 0.8199 (m-30) REVERT: A 563 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8269 (mmmt) REVERT: A 564 LYS cc_start: 0.8882 (tppt) cc_final: 0.8413 (tppt) REVERT: A 590 LYS cc_start: 0.8489 (pptt) cc_final: 0.8256 (tmmt) REVERT: A 677 ARG cc_start: 0.8397 (ttt180) cc_final: 0.7891 (tpp80) REVERT: A 678 MET cc_start: 0.8055 (mmm) cc_final: 0.7804 (mmm) REVERT: A 687 ASP cc_start: 0.8592 (t0) cc_final: 0.8197 (t0) REVERT: A 697 ASP cc_start: 0.8568 (m-30) cc_final: 0.6942 (t0) REVERT: A 701 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 715 LYS cc_start: 0.8482 (mttm) cc_final: 0.8261 (mtpp) REVERT: A 724 ASP cc_start: 0.8434 (m-30) cc_final: 0.8170 (m-30) REVERT: A 727 LEU cc_start: 0.8782 (mm) cc_final: 0.7797 (mt) REVERT: A 728 HIS cc_start: 0.8874 (t70) cc_final: 0.8521 (t70) REVERT: A 730 GLN cc_start: 0.8405 (pp30) cc_final: 0.8120 (pp30) REVERT: A 731 ASN cc_start: 0.8529 (m110) cc_final: 0.8053 (m110) REVERT: B 27 TYR cc_start: 0.8767 (m-10) cc_final: 0.8089 (m-10) REVERT: B 37 GLU cc_start: 0.8163 (pp20) cc_final: 0.7764 (pp20) REVERT: B 105 TYR cc_start: 0.7306 (m-80) cc_final: 0.6877 (m-80) REVERT: B 122 PHE cc_start: 0.8233 (m-80) cc_final: 0.7744 (m-80) REVERT: B 124 ILE cc_start: 0.8729 (mm) cc_final: 0.8346 (pt) REVERT: B 125 LEU cc_start: 0.8802 (mt) cc_final: 0.8504 (mt) REVERT: B 137 SER cc_start: 0.7805 (t) cc_final: 0.7439 (t) REVERT: B 143 VAL cc_start: 0.7837 (m) cc_final: 0.7520 (m) REVERT: B 144 VAL cc_start: 0.8680 (p) cc_final: 0.8179 (m) REVERT: B 147 MET cc_start: 0.9057 (mtt) cc_final: 0.8606 (mtt) REVERT: B 199 ILE cc_start: 0.8580 (tp) cc_final: 0.8350 (tp) REVERT: B 207 GLN cc_start: 0.8837 (tt0) cc_final: 0.8490 (tm-30) REVERT: B 210 PHE cc_start: 0.7045 (p90) cc_final: 0.6718 (p90) REVERT: B 230 GLN cc_start: 0.8376 (tp40) cc_final: 0.7792 (tp40) REVERT: B 233 VAL cc_start: 0.9101 (p) cc_final: 0.8825 (m) REVERT: B 235 GLN cc_start: 0.8342 (pp30) cc_final: 0.8140 (pp30) REVERT: B 236 LEU cc_start: 0.8745 (tp) cc_final: 0.8411 (tp) REVERT: B 237 LYS cc_start: 0.9057 (pttt) cc_final: 0.8263 (pttp) REVERT: B 238 ILE cc_start: 0.8667 (tp) cc_final: 0.8265 (pt) REVERT: B 241 ASN cc_start: 0.8050 (m110) cc_final: 0.7444 (m110) REVERT: B 250 ILE cc_start: 0.8682 (pt) cc_final: 0.8440 (tp) REVERT: B 251 LEU cc_start: 0.8696 (mm) cc_final: 0.6669 (mm) REVERT: B 255 TYR cc_start: 0.7586 (m-10) cc_final: 0.6962 (m-80) REVERT: B 259 GLU cc_start: 0.8674 (tt0) cc_final: 0.7689 (tt0) REVERT: B 303 GLU cc_start: 0.8962 (mp0) cc_final: 0.8635 (pm20) REVERT: B 318 ASN cc_start: 0.8574 (t0) cc_final: 0.8255 (t0) REVERT: B 319 LEU cc_start: 0.8673 (mt) cc_final: 0.8203 (pp) REVERT: B 323 TYR cc_start: 0.8176 (m-80) cc_final: 0.7921 (m-80) REVERT: B 443 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6882 (tm-30) REVERT: B 455 ILE cc_start: 0.8694 (mt) cc_final: 0.8265 (mp) REVERT: B 459 LYS cc_start: 0.8751 (mmtt) cc_final: 0.7720 (mmtt) REVERT: B 463 MET cc_start: 0.7305 (mmm) cc_final: 0.6390 (mmm) REVERT: B 477 THR cc_start: 0.8186 (m) cc_final: 0.7834 (p) REVERT: B 484 PHE cc_start: 0.8464 (t80) cc_final: 0.7890 (t80) REVERT: B 488 MET cc_start: 0.7833 (tpp) cc_final: 0.6554 (tpp) REVERT: B 491 ILE cc_start: 0.8957 (mt) cc_final: 0.8574 (mm) REVERT: B 492 LEU cc_start: 0.8716 (mt) cc_final: 0.7296 (mt) REVERT: B 494 LEU cc_start: 0.9147 (mt) cc_final: 0.8766 (mm) REVERT: B 496 LEU cc_start: 0.7982 (mt) cc_final: 0.7647 (mm) REVERT: B 512 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8209 (mtm-85) REVERT: B 514 GLN cc_start: 0.8894 (tt0) cc_final: 0.8410 (tm-30) REVERT: B 537 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7793 (mtmt) REVERT: B 563 LYS cc_start: 0.9013 (tppt) cc_final: 0.8154 (tppt) REVERT: B 577 VAL cc_start: 0.9002 (m) cc_final: 0.8743 (p) REVERT: B 578 TYR cc_start: 0.7945 (t80) cc_final: 0.6204 (t80) REVERT: B 677 ARG cc_start: 0.8599 (ttt180) cc_final: 0.7951 (ttm-80) REVERT: B 678 MET cc_start: 0.8195 (mmm) cc_final: 0.7815 (mmm) REVERT: B 682 GLU cc_start: 0.8369 (tp30) cc_final: 0.7853 (tp30) REVERT: B 684 GLN cc_start: 0.9164 (tp40) cc_final: 0.8958 (tp-100) REVERT: B 685 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7618 (mtm180) REVERT: B 701 GLU cc_start: 0.7861 (mp0) cc_final: 0.7637 (mp0) REVERT: B 716 ASP cc_start: 0.8163 (p0) cc_final: 0.7369 (t0) REVERT: B 719 PHE cc_start: 0.7730 (m-80) cc_final: 0.7384 (m-10) REVERT: B 720 LEU cc_start: 0.9120 (mp) cc_final: 0.8762 (mt) REVERT: B 727 LEU cc_start: 0.9001 (mt) cc_final: 0.8750 (mt) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.2891 time to fit residues: 137.3052 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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: 0.9990 chunk 121 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 535 HIS A 730 GLN B 289 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090994 restraints weight = 25867.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094283 restraints weight = 15805.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096587 restraints weight = 10820.977| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10395 Z= 0.154 Angle : 0.632 13.049 14128 Z= 0.322 Chirality : 0.044 0.396 1716 Planarity : 0.004 0.046 1757 Dihedral : 4.004 23.033 1415 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.09 % Allowed : 2.85 % 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: -0.96 (0.23), residues: 1319 helix: 0.46 (0.18), residues: 816 sheet: -1.79 (1.00), residues: 34 loop : -2.53 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 74 HIS 0.002 0.000 HIS A 723 PHE 0.026 0.001 PHE A 115 TYR 0.018 0.001 TYR A 118 ARG 0.005 0.001 ARG B 587 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 546) hydrogen bonds : angle 3.89257 ( 1596) covalent geometry : bond 0.00319 (10395) covalent geometry : angle 0.63206 (14128) *********************** 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 373 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8471 (t80) cc_final: 0.8001 (t80) REVERT: A 66 LYS cc_start: 0.8960 (tptt) cc_final: 0.8459 (tppt) REVERT: A 96 LEU cc_start: 0.8811 (mt) cc_final: 0.8461 (mm) REVERT: A 103 MET cc_start: 0.8387 (mtm) cc_final: 0.8144 (mpp) REVERT: A 105 TYR cc_start: 0.8645 (m-80) cc_final: 0.8312 (m-80) REVERT: A 118 TYR cc_start: 0.8155 (m-80) cc_final: 0.7629 (m-80) REVERT: A 119 SER cc_start: 0.8797 (t) cc_final: 0.8256 (p) REVERT: A 121 PHE cc_start: 0.7704 (t80) cc_final: 0.7356 (t80) REVERT: A 194 LEU cc_start: 0.8492 (tp) cc_final: 0.8186 (mm) REVERT: A 211 ILE cc_start: 0.9037 (tt) cc_final: 0.8725 (tp) REVERT: A 230 GLN cc_start: 0.8856 (mt0) cc_final: 0.8365 (tp-100) REVERT: A 234 SER cc_start: 0.9211 (m) cc_final: 0.8481 (p) REVERT: A 235 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8245 (mm-40) REVERT: A 237 LYS cc_start: 0.8947 (pttp) cc_final: 0.8483 (pttm) REVERT: A 245 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8338 (mmmt) REVERT: A 252 SER cc_start: 0.8202 (p) cc_final: 0.7713 (m) REVERT: A 262 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 272 PHE cc_start: 0.8203 (t80) cc_final: 0.7792 (t80) REVERT: A 276 LEU cc_start: 0.8695 (pp) cc_final: 0.8366 (pp) REVERT: A 279 ILE cc_start: 0.9121 (mm) cc_final: 0.8765 (mm) REVERT: A 282 CYS cc_start: 0.8786 (t) cc_final: 0.8349 (p) REVERT: A 283 MET cc_start: 0.7731 (mmp) cc_final: 0.7397 (mmp) REVERT: A 285 VAL cc_start: 0.8681 (m) cc_final: 0.8404 (p) REVERT: A 286 LYS cc_start: 0.9065 (tppt) cc_final: 0.8632 (tppt) REVERT: A 293 LYS cc_start: 0.8329 (tppt) cc_final: 0.7841 (tppt) REVERT: A 305 ILE cc_start: 0.8679 (tp) cc_final: 0.8306 (pt) REVERT: A 309 ILE cc_start: 0.8897 (tp) cc_final: 0.8615 (pt) REVERT: A 324 ASN cc_start: 0.8218 (t0) cc_final: 0.7877 (t0) REVERT: A 345 LEU cc_start: 0.8478 (mt) cc_final: 0.7679 (mt) REVERT: A 349 MET cc_start: 0.7110 (mtm) cc_final: 0.6664 (mtm) REVERT: A 353 SER cc_start: 0.8981 (m) cc_final: 0.8630 (p) REVERT: A 369 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8074 (mmtt) REVERT: A 371 TYR cc_start: 0.8335 (m-80) cc_final: 0.7773 (m-80) REVERT: A 385 PHE cc_start: 0.8121 (t80) cc_final: 0.7312 (t80) REVERT: A 388 PHE cc_start: 0.8956 (m-80) cc_final: 0.8691 (m-80) REVERT: A 392 ASN cc_start: 0.9261 (m-40) cc_final: 0.8935 (m-40) REVERT: A 394 PHE cc_start: 0.8276 (t80) cc_final: 0.7735 (t80) REVERT: A 397 PHE cc_start: 0.7886 (t80) cc_final: 0.7660 (t80) REVERT: A 414 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 432 MET cc_start: 0.8229 (tpt) cc_final: 0.7851 (tpt) REVERT: A 433 VAL cc_start: 0.8868 (p) cc_final: 0.8654 (m) REVERT: A 443 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 454 VAL cc_start: 0.8987 (t) cc_final: 0.8756 (t) REVERT: A 458 LEU cc_start: 0.8694 (mt) cc_final: 0.8451 (mt) REVERT: A 459 LYS cc_start: 0.8456 (tppp) cc_final: 0.6612 (tppp) REVERT: A 461 MET cc_start: 0.8976 (mtp) cc_final: 0.8757 (mtp) REVERT: A 463 MET cc_start: 0.8061 (mmp) cc_final: 0.6870 (mmp) REVERT: A 467 ASP cc_start: 0.7968 (p0) cc_final: 0.7711 (p0) REVERT: A 470 ARG cc_start: 0.7987 (ptp-170) cc_final: 0.7740 (ptt-90) REVERT: A 473 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8424 (mtpt) REVERT: A 486 CYS cc_start: 0.8804 (t) cc_final: 0.8270 (p) REVERT: A 487 ILE cc_start: 0.9004 (mt) cc_final: 0.8687 (pt) REVERT: A 496 LEU cc_start: 0.8987 (tp) cc_final: 0.8688 (tp) REVERT: A 514 GLN cc_start: 0.8333 (tt0) cc_final: 0.7803 (tm-30) REVERT: A 530 TYR cc_start: 0.8265 (m-10) cc_final: 0.7854 (m-80) REVERT: A 540 GLU cc_start: 0.7714 (pt0) cc_final: 0.7132 (pm20) REVERT: A 549 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7143 (tpp-160) REVERT: A 560 ASP cc_start: 0.8466 (m-30) cc_final: 0.7919 (m-30) REVERT: A 563 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8198 (mmmt) REVERT: A 564 LYS cc_start: 0.8901 (tppt) cc_final: 0.8408 (tppt) REVERT: A 677 ARG cc_start: 0.8383 (ttt180) cc_final: 0.7873 (tpp80) REVERT: A 678 MET cc_start: 0.8079 (mmm) cc_final: 0.7717 (mmm) REVERT: A 687 ASP cc_start: 0.8514 (t0) cc_final: 0.8107 (t0) REVERT: A 697 ASP cc_start: 0.8577 (m-30) cc_final: 0.8324 (p0) REVERT: A 701 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 705 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7605 (tp-100) REVERT: A 715 LYS cc_start: 0.8374 (mttm) cc_final: 0.7898 (mttm) REVERT: A 723 HIS cc_start: 0.8205 (t70) cc_final: 0.7861 (t-90) REVERT: A 724 ASP cc_start: 0.8458 (m-30) cc_final: 0.8174 (m-30) REVERT: A 727 LEU cc_start: 0.8888 (mm) cc_final: 0.7341 (mt) REVERT: A 728 HIS cc_start: 0.8867 (t70) cc_final: 0.8448 (t70) REVERT: A 731 ASN cc_start: 0.8575 (m110) cc_final: 0.7866 (m-40) REVERT: B 27 TYR cc_start: 0.8772 (m-10) cc_final: 0.8116 (m-10) REVERT: B 30 LEU cc_start: 0.8577 (pt) cc_final: 0.8235 (pt) REVERT: B 37 GLU cc_start: 0.8195 (pp20) cc_final: 0.7907 (pp20) REVERT: B 105 TYR cc_start: 0.7275 (m-80) cc_final: 0.6894 (m-80) REVERT: B 122 PHE cc_start: 0.8272 (m-80) cc_final: 0.7738 (m-80) REVERT: B 124 ILE cc_start: 0.8767 (mm) cc_final: 0.8341 (pt) REVERT: B 125 LEU cc_start: 0.8800 (mt) cc_final: 0.8515 (mt) REVERT: B 137 SER cc_start: 0.7833 (t) cc_final: 0.7524 (t) REVERT: B 144 VAL cc_start: 0.8596 (p) cc_final: 0.8187 (m) REVERT: B 147 MET cc_start: 0.8973 (mtt) cc_final: 0.8630 (mtt) REVERT: B 155 MET cc_start: 0.6353 (ptp) cc_final: 0.6146 (ptp) REVERT: B 186 VAL cc_start: 0.9054 (p) cc_final: 0.8784 (m) REVERT: B 199 ILE cc_start: 0.8519 (tp) cc_final: 0.8287 (tp) REVERT: B 207 GLN cc_start: 0.8820 (tt0) cc_final: 0.8435 (tm-30) REVERT: B 210 PHE cc_start: 0.6984 (p90) cc_final: 0.6705 (p90) REVERT: B 213 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7078 (mtp85) REVERT: B 236 LEU cc_start: 0.8773 (tp) cc_final: 0.8504 (tp) REVERT: B 237 LYS cc_start: 0.9032 (pttt) cc_final: 0.8511 (pttp) REVERT: B 238 ILE cc_start: 0.8673 (tp) cc_final: 0.8265 (pt) REVERT: B 241 ASN cc_start: 0.8009 (m110) cc_final: 0.7390 (m110) REVERT: B 250 ILE cc_start: 0.8703 (pt) cc_final: 0.8428 (tp) REVERT: B 251 LEU cc_start: 0.8629 (mm) cc_final: 0.6660 (mm) REVERT: B 255 TYR cc_start: 0.7638 (m-10) cc_final: 0.7004 (m-80) REVERT: B 259 GLU cc_start: 0.8599 (tt0) cc_final: 0.8333 (tm-30) REVERT: B 260 ILE cc_start: 0.9218 (mm) cc_final: 0.8855 (mt) REVERT: B 261 PHE cc_start: 0.8329 (m-10) cc_final: 0.8064 (m-80) REVERT: B 303 GLU cc_start: 0.8939 (mp0) cc_final: 0.8603 (pm20) REVERT: B 318 ASN cc_start: 0.8508 (t0) cc_final: 0.8225 (t0) REVERT: B 319 LEU cc_start: 0.8648 (mt) cc_final: 0.8331 (mt) REVERT: B 321 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8342 (ttpp) REVERT: B 322 ASN cc_start: 0.8080 (m110) cc_final: 0.7560 (t0) REVERT: B 323 TYR cc_start: 0.8176 (m-80) cc_final: 0.6995 (m-80) REVERT: B 440 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7044 (mmm160) REVERT: B 455 ILE cc_start: 0.8697 (mt) cc_final: 0.8311 (mm) REVERT: B 459 LYS cc_start: 0.8753 (mmtt) cc_final: 0.7646 (mmtt) REVERT: B 463 MET cc_start: 0.7367 (mmm) cc_final: 0.6456 (mmm) REVERT: B 473 LYS cc_start: 0.8431 (mttp) cc_final: 0.7468 (mttp) REVERT: B 477 THR cc_start: 0.8151 (m) cc_final: 0.7782 (p) REVERT: B 478 ASP cc_start: 0.8450 (p0) cc_final: 0.8191 (p0) REVERT: B 484 PHE cc_start: 0.8402 (t80) cc_final: 0.7864 (t80) REVERT: B 488 MET cc_start: 0.7736 (tpp) cc_final: 0.6472 (tpp) REVERT: B 491 ILE cc_start: 0.8934 (mt) cc_final: 0.8578 (mm) REVERT: B 492 LEU cc_start: 0.8688 (mt) cc_final: 0.7276 (mt) REVERT: B 494 LEU cc_start: 0.9134 (mt) cc_final: 0.8524 (pt) REVERT: B 495 ASP cc_start: 0.7488 (p0) cc_final: 0.7268 (p0) REVERT: B 496 LEU cc_start: 0.7983 (mt) cc_final: 0.7208 (mt) REVERT: B 512 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8196 (mtm-85) REVERT: B 514 GLN cc_start: 0.8837 (tt0) cc_final: 0.8398 (tm-30) REVERT: B 537 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7830 (mtmt) REVERT: B 546 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8114 (mmtm) REVERT: B 563 LYS cc_start: 0.8987 (tppt) cc_final: 0.7910 (tppt) REVERT: B 567 ASN cc_start: 0.8263 (m-40) cc_final: 0.7690 (m110) REVERT: B 576 ARG cc_start: 0.8346 (ptt90) cc_final: 0.8051 (ptt90) REVERT: B 577 VAL cc_start: 0.9020 (m) cc_final: 0.8730 (p) REVERT: B 578 TYR cc_start: 0.7914 (t80) cc_final: 0.6426 (t80) REVERT: B 583 LYS cc_start: 0.8623 (ptmm) cc_final: 0.8148 (ptmm) REVERT: B 586 ARG cc_start: 0.7963 (pmt-80) cc_final: 0.7735 (pmt-80) REVERT: B 590 LYS cc_start: 0.8540 (pttp) cc_final: 0.8161 (pttm) REVERT: B 594 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8307 (ptpt) REVERT: B 674 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8178 (ttm110) REVERT: B 677 ARG cc_start: 0.8583 (ttt180) cc_final: 0.8124 (ttm-80) REVERT: B 678 MET cc_start: 0.8176 (mmm) cc_final: 0.7824 (mmm) REVERT: B 682 GLU cc_start: 0.8320 (tp30) cc_final: 0.7798 (tp30) REVERT: B 685 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7565 (mtm180) REVERT: B 705 GLN cc_start: 0.8548 (tt0) cc_final: 0.8163 (pp30) REVERT: B 719 PHE cc_start: 0.7816 (m-80) cc_final: 0.7507 (m-10) REVERT: B 720 LEU cc_start: 0.9132 (mp) cc_final: 0.8814 (mt) REVERT: B 727 LEU cc_start: 0.8970 (mt) cc_final: 0.8402 (mt) REVERT: B 730 GLN cc_start: 0.8924 (tt0) cc_final: 0.8332 (tm-30) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.3001 time to fit residues: 147.9706 Evaluate side-chains 347 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 289 ASN B 375 HIS ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089172 restraints weight = 26226.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092400 restraints weight = 15953.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094774 restraints weight = 11003.418| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10395 Z= 0.187 Angle : 0.645 10.266 14128 Z= 0.335 Chirality : 0.044 0.293 1716 Planarity : 0.004 0.047 1757 Dihedral : 4.162 23.569 1415 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.23), residues: 1319 helix: 0.42 (0.18), residues: 839 sheet: -1.72 (1.00), residues: 34 loop : -2.54 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 74 HIS 0.006 0.001 HIS A 723 PHE 0.027 0.001 PHE A 115 TYR 0.016 0.001 TYR A 118 ARG 0.005 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 546) hydrogen bonds : angle 3.93199 ( 1596) covalent geometry : bond 0.00371 (10395) covalent geometry : angle 0.64500 (14128) *********************** 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 372 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8506 (t80) cc_final: 0.8123 (t80) REVERT: A 38 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7682 (ttm110) REVERT: A 96 LEU cc_start: 0.8780 (mt) cc_final: 0.8456 (mm) REVERT: A 99 THR cc_start: 0.9000 (t) cc_final: 0.8301 (t) REVERT: A 103 MET cc_start: 0.8552 (mtm) cc_final: 0.8225 (mpp) REVERT: A 105 TYR cc_start: 0.8592 (m-80) cc_final: 0.8303 (m-80) REVERT: A 118 TYR cc_start: 0.8229 (m-80) cc_final: 0.7689 (m-80) REVERT: A 119 SER cc_start: 0.8794 (t) cc_final: 0.8291 (p) REVERT: A 121 PHE cc_start: 0.7765 (t80) cc_final: 0.7354 (t80) REVERT: A 181 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7284 (tpp80) REVERT: A 194 LEU cc_start: 0.8495 (tp) cc_final: 0.8229 (mm) REVERT: A 211 ILE cc_start: 0.9082 (tt) cc_final: 0.8792 (tp) REVERT: A 230 GLN cc_start: 0.8787 (mt0) cc_final: 0.8308 (tp-100) REVERT: A 234 SER cc_start: 0.9180 (m) cc_final: 0.8828 (p) REVERT: A 235 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8291 (mm-40) REVERT: A 237 LYS cc_start: 0.8968 (pttp) cc_final: 0.8334 (ptpt) REVERT: A 252 SER cc_start: 0.8287 (p) cc_final: 0.7847 (m) REVERT: A 262 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 272 PHE cc_start: 0.8199 (t80) cc_final: 0.7845 (t80) REVERT: A 276 LEU cc_start: 0.8732 (pp) cc_final: 0.8495 (pp) REVERT: A 279 ILE cc_start: 0.9106 (mm) cc_final: 0.8614 (tp) REVERT: A 281 VAL cc_start: 0.8883 (m) cc_final: 0.8661 (p) REVERT: A 282 CYS cc_start: 0.8775 (t) cc_final: 0.8348 (p) REVERT: A 283 MET cc_start: 0.7702 (mmp) cc_final: 0.7313 (mmp) REVERT: A 285 VAL cc_start: 0.8753 (m) cc_final: 0.8485 (p) REVERT: A 286 LYS cc_start: 0.9072 (tppt) cc_final: 0.8587 (tppt) REVERT: A 293 LYS cc_start: 0.8340 (tppt) cc_final: 0.7858 (tppt) REVERT: A 309 ILE cc_start: 0.8918 (tp) cc_final: 0.8649 (pt) REVERT: A 321 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8238 (ttpp) REVERT: A 324 ASN cc_start: 0.8281 (t0) cc_final: 0.7971 (t0) REVERT: A 345 LEU cc_start: 0.8482 (mt) cc_final: 0.7655 (mt) REVERT: A 346 PHE cc_start: 0.8055 (m-10) cc_final: 0.7750 (m-10) REVERT: A 349 MET cc_start: 0.7201 (mtm) cc_final: 0.6671 (mtm) REVERT: A 353 SER cc_start: 0.8964 (m) cc_final: 0.8675 (p) REVERT: A 369 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8623 (tppt) REVERT: A 371 TYR cc_start: 0.8305 (m-80) cc_final: 0.7714 (m-80) REVERT: A 385 PHE cc_start: 0.8181 (t80) cc_final: 0.7333 (t80) REVERT: A 388 PHE cc_start: 0.8977 (m-80) cc_final: 0.8774 (m-80) REVERT: A 392 ASN cc_start: 0.9282 (m-40) cc_final: 0.8954 (m-40) REVERT: A 394 PHE cc_start: 0.8334 (t80) cc_final: 0.7790 (t80) REVERT: A 397 PHE cc_start: 0.7922 (t80) cc_final: 0.7685 (t80) REVERT: A 414 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 432 MET cc_start: 0.8277 (tpt) cc_final: 0.7919 (tpt) REVERT: A 433 VAL cc_start: 0.8908 (p) cc_final: 0.8688 (m) REVERT: A 443 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 447 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8958 (mtmt) REVERT: A 454 VAL cc_start: 0.9022 (t) cc_final: 0.8766 (t) REVERT: A 458 LEU cc_start: 0.8777 (mt) cc_final: 0.8564 (mt) REVERT: A 459 LYS cc_start: 0.8452 (tppp) cc_final: 0.6500 (tppp) REVERT: A 463 MET cc_start: 0.7993 (mmp) cc_final: 0.6903 (mmp) REVERT: A 467 ASP cc_start: 0.8019 (p0) cc_final: 0.7753 (p0) REVERT: A 470 ARG cc_start: 0.7930 (ptp-170) cc_final: 0.7352 (ptt-90) REVERT: A 472 TRP cc_start: 0.8444 (t-100) cc_final: 0.7777 (t-100) REVERT: A 473 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8625 (pttp) REVERT: A 486 CYS cc_start: 0.8898 (t) cc_final: 0.8323 (p) REVERT: A 487 ILE cc_start: 0.9033 (mt) cc_final: 0.8707 (pt) REVERT: A 496 LEU cc_start: 0.9027 (tp) cc_final: 0.8729 (tp) REVERT: A 514 GLN cc_start: 0.8376 (tt0) cc_final: 0.7870 (tm-30) REVERT: A 530 TYR cc_start: 0.8253 (m-10) cc_final: 0.7947 (m-10) REVERT: A 540 GLU cc_start: 0.7696 (pt0) cc_final: 0.7128 (pm20) REVERT: A 549 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7053 (tpp-160) REVERT: A 560 ASP cc_start: 0.8454 (m-30) cc_final: 0.8038 (m-30) REVERT: A 563 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8202 (mmmt) REVERT: A 564 LYS cc_start: 0.8928 (tppt) cc_final: 0.8498 (tppt) REVERT: A 580 LYS cc_start: 0.7841 (tttt) cc_final: 0.7357 (tttp) REVERT: A 590 LYS cc_start: 0.8548 (pptt) cc_final: 0.8253 (tmmt) REVERT: A 677 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7884 (tpp80) REVERT: A 687 ASP cc_start: 0.8544 (t0) cc_final: 0.8132 (t0) REVERT: A 697 ASP cc_start: 0.8577 (m-30) cc_final: 0.8360 (p0) REVERT: A 701 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 705 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7623 (tp-100) REVERT: A 724 ASP cc_start: 0.8442 (m-30) cc_final: 0.8156 (m-30) REVERT: A 727 LEU cc_start: 0.8810 (mm) cc_final: 0.8301 (mm) REVERT: A 728 HIS cc_start: 0.8861 (t70) cc_final: 0.8586 (t70) REVERT: A 731 ASN cc_start: 0.8547 (m110) cc_final: 0.8194 (m110) REVERT: B 27 TYR cc_start: 0.8857 (m-10) cc_final: 0.8278 (m-10) REVERT: B 30 LEU cc_start: 0.8390 (pt) cc_final: 0.8187 (pt) REVERT: B 33 GLN cc_start: 0.8304 (pp30) cc_final: 0.7945 (pp30) REVERT: B 39 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7983 (mtt-85) REVERT: B 105 TYR cc_start: 0.7426 (m-80) cc_final: 0.7138 (m-80) REVERT: B 122 PHE cc_start: 0.8319 (m-80) cc_final: 0.7765 (m-80) REVERT: B 124 ILE cc_start: 0.8826 (mm) cc_final: 0.8413 (pt) REVERT: B 125 LEU cc_start: 0.8817 (mt) cc_final: 0.8528 (mt) REVERT: B 137 SER cc_start: 0.7885 (t) cc_final: 0.7551 (t) REVERT: B 147 MET cc_start: 0.9028 (mtt) cc_final: 0.8678 (mmp) REVERT: B 186 VAL cc_start: 0.8998 (p) cc_final: 0.8646 (m) REVERT: B 196 VAL cc_start: 0.9007 (t) cc_final: 0.8776 (t) REVERT: B 199 ILE cc_start: 0.8553 (tp) cc_final: 0.8284 (tp) REVERT: B 200 GLN cc_start: 0.8579 (mt0) cc_final: 0.8355 (mt0) REVERT: B 207 GLN cc_start: 0.8892 (tt0) cc_final: 0.8462 (tm-30) REVERT: B 210 PHE cc_start: 0.7087 (p90) cc_final: 0.6808 (p90) REVERT: B 213 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7197 (mtp180) REVERT: B 230 GLN cc_start: 0.8489 (pp30) cc_final: 0.7946 (pp30) REVERT: B 236 LEU cc_start: 0.8748 (tp) cc_final: 0.8495 (tp) REVERT: B 237 LYS cc_start: 0.9009 (pttt) cc_final: 0.8536 (pttp) REVERT: B 238 ILE cc_start: 0.8676 (tp) cc_final: 0.8284 (pt) REVERT: B 241 ASN cc_start: 0.8001 (m110) cc_final: 0.7437 (m110) REVERT: B 250 ILE cc_start: 0.8678 (pt) cc_final: 0.8450 (tp) REVERT: B 251 LEU cc_start: 0.8608 (mm) cc_final: 0.6601 (mm) REVERT: B 255 TYR cc_start: 0.7647 (m-10) cc_final: 0.7026 (m-80) REVERT: B 259 GLU cc_start: 0.8573 (tt0) cc_final: 0.8338 (tm-30) REVERT: B 260 ILE cc_start: 0.9215 (mm) cc_final: 0.8866 (mt) REVERT: B 271 ASP cc_start: 0.8377 (t0) cc_final: 0.8100 (t0) REVERT: B 303 GLU cc_start: 0.8995 (mp0) cc_final: 0.8600 (mp0) REVERT: B 318 ASN cc_start: 0.8544 (t0) cc_final: 0.8188 (t0) REVERT: B 321 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8444 (ttpp) REVERT: B 322 ASN cc_start: 0.8128 (m110) cc_final: 0.7530 (t0) REVERT: B 323 TYR cc_start: 0.8199 (m-80) cc_final: 0.6946 (m-80) REVERT: B 440 ARG cc_start: 0.7659 (mmm160) cc_final: 0.6990 (mmm160) REVERT: B 455 ILE cc_start: 0.8814 (mt) cc_final: 0.8263 (mp) REVERT: B 459 LYS cc_start: 0.8711 (mmtt) cc_final: 0.7551 (mmtt) REVERT: B 463 MET cc_start: 0.7375 (mmm) cc_final: 0.6383 (mmm) REVERT: B 473 LYS cc_start: 0.8474 (mttp) cc_final: 0.7591 (pttt) REVERT: B 477 THR cc_start: 0.8155 (m) cc_final: 0.7809 (p) REVERT: B 478 ASP cc_start: 0.8499 (p0) cc_final: 0.8222 (p0) REVERT: B 482 TRP cc_start: 0.8440 (t60) cc_final: 0.8193 (t60) REVERT: B 484 PHE cc_start: 0.8419 (t80) cc_final: 0.7858 (t80) REVERT: B 488 MET cc_start: 0.7778 (tpp) cc_final: 0.6452 (tpp) REVERT: B 491 ILE cc_start: 0.8944 (mt) cc_final: 0.8568 (mm) REVERT: B 492 LEU cc_start: 0.8768 (mt) cc_final: 0.7248 (mt) REVERT: B 496 LEU cc_start: 0.7975 (mt) cc_final: 0.7712 (mt) REVERT: B 512 ARG cc_start: 0.8565 (mtm180) cc_final: 0.8271 (mtm-85) REVERT: B 514 GLN cc_start: 0.8806 (tt0) cc_final: 0.8366 (tm-30) REVERT: B 563 LYS cc_start: 0.9008 (tppt) cc_final: 0.7834 (tppt) REVERT: B 567 ASN cc_start: 0.8331 (m-40) cc_final: 0.7643 (m110) REVERT: B 577 VAL cc_start: 0.8995 (m) cc_final: 0.8735 (p) REVERT: B 578 TYR cc_start: 0.7918 (t80) cc_final: 0.6136 (t80) REVERT: B 582 LEU cc_start: 0.9025 (mt) cc_final: 0.8605 (mt) REVERT: B 583 LYS cc_start: 0.8619 (ptmm) cc_final: 0.8087 (ptmm) REVERT: B 674 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8161 (ttm110) REVERT: B 677 ARG cc_start: 0.8578 (ttt180) cc_final: 0.8088 (ttm-80) REVERT: B 678 MET cc_start: 0.8183 (mmm) cc_final: 0.7856 (mmm) REVERT: B 682 GLU cc_start: 0.8320 (tp30) cc_final: 0.7810 (tp30) REVERT: B 685 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7561 (mtm180) REVERT: B 687 ASP cc_start: 0.8259 (t0) cc_final: 0.7909 (t0) REVERT: B 691 TYR cc_start: 0.7732 (m-80) cc_final: 0.7008 (m-80) REVERT: B 701 GLU cc_start: 0.7785 (mp0) cc_final: 0.7531 (mp0) REVERT: B 702 LYS cc_start: 0.7649 (tptp) cc_final: 0.7363 (tptp) REVERT: B 705 GLN cc_start: 0.8582 (tt0) cc_final: 0.8173 (pp30) REVERT: B 716 ASP cc_start: 0.8208 (p0) cc_final: 0.7355 (t0) REVERT: B 719 PHE cc_start: 0.7865 (m-80) cc_final: 0.7587 (m-10) REVERT: B 720 LEU cc_start: 0.9199 (mp) cc_final: 0.8866 (mt) REVERT: B 727 LEU cc_start: 0.9016 (mt) cc_final: 0.8499 (mt) REVERT: B 730 GLN cc_start: 0.8968 (tt0) cc_final: 0.8400 (tm-30) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.3626 time to fit residues: 178.3146 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 : 2.192 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 567 ASN B 289 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090649 restraints weight = 26290.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093985 restraints weight = 16008.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096372 restraints weight = 10988.950| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5072 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= 0.140 Angle : 0.622 9.295 14128 Z= 0.320 Chirality : 0.044 0.300 1716 Planarity : 0.004 0.079 1757 Dihedral : 4.154 24.370 1415 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.23), residues: 1319 helix: 0.48 (0.18), residues: 833 sheet: -1.63 (1.02), residues: 34 loop : -2.45 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 482 HIS 0.004 0.000 HIS A 535 PHE 0.026 0.001 PHE A 115 TYR 0.017 0.001 TYR A 118 ARG 0.004 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 546) hydrogen bonds : angle 3.86593 ( 1596) covalent geometry : bond 0.00302 (10395) covalent geometry : angle 0.62231 (14128) *********************** 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 368 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8489 (t80) cc_final: 0.8175 (t80) REVERT: A 38 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7483 (ttm110) REVERT: A 59 LYS cc_start: 0.8492 (tptt) cc_final: 0.8223 (mmmt) REVERT: A 66 LYS cc_start: 0.8999 (tptt) cc_final: 0.8795 (tptt) REVERT: A 96 LEU cc_start: 0.8761 (mt) cc_final: 0.8442 (mm) REVERT: A 99 THR cc_start: 0.8967 (t) cc_final: 0.8079 (t) REVERT: A 103 MET cc_start: 0.8536 (mtm) cc_final: 0.8090 (mpp) REVERT: A 105 TYR cc_start: 0.8617 (m-80) cc_final: 0.8337 (m-80) REVERT: A 118 TYR cc_start: 0.8247 (m-80) cc_final: 0.7723 (m-80) REVERT: A 119 SER cc_start: 0.8759 (t) cc_final: 0.8278 (p) REVERT: A 121 PHE cc_start: 0.7704 (t80) cc_final: 0.7356 (t80) REVERT: A 194 LEU cc_start: 0.8396 (tp) cc_final: 0.8068 (mm) REVERT: A 211 ILE cc_start: 0.9050 (tt) cc_final: 0.8774 (tp) REVERT: A 230 GLN cc_start: 0.8775 (mt0) cc_final: 0.8225 (tp40) REVERT: A 234 SER cc_start: 0.9189 (m) cc_final: 0.8607 (p) REVERT: A 235 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8309 (mm-40) REVERT: A 237 LYS cc_start: 0.8958 (pttp) cc_final: 0.8499 (pttp) REVERT: A 252 SER cc_start: 0.8244 (p) cc_final: 0.7797 (m) REVERT: A 262 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 272 PHE cc_start: 0.8123 (t80) cc_final: 0.7804 (t80) REVERT: A 276 LEU cc_start: 0.8715 (pp) cc_final: 0.8470 (pp) REVERT: A 279 ILE cc_start: 0.9100 (mm) cc_final: 0.8636 (tp) REVERT: A 281 VAL cc_start: 0.8883 (m) cc_final: 0.8682 (p) REVERT: A 282 CYS cc_start: 0.8732 (t) cc_final: 0.8348 (p) REVERT: A 283 MET cc_start: 0.7644 (mmp) cc_final: 0.7264 (mmp) REVERT: A 286 LYS cc_start: 0.8932 (tppt) cc_final: 0.8648 (tppt) REVERT: A 293 LYS cc_start: 0.8334 (tppt) cc_final: 0.7856 (tppt) REVERT: A 305 ILE cc_start: 0.8637 (tp) cc_final: 0.8204 (pt) REVERT: A 309 ILE cc_start: 0.8906 (tp) cc_final: 0.8615 (pt) REVERT: A 324 ASN cc_start: 0.8209 (t0) cc_final: 0.7895 (t0) REVERT: A 345 LEU cc_start: 0.8530 (mt) cc_final: 0.7638 (pt) REVERT: A 353 SER cc_start: 0.8941 (m) cc_final: 0.8677 (p) REVERT: A 369 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8622 (tppt) REVERT: A 371 TYR cc_start: 0.8350 (m-80) cc_final: 0.7750 (m-80) REVERT: A 385 PHE cc_start: 0.8085 (t80) cc_final: 0.7400 (t80) REVERT: A 388 PHE cc_start: 0.8951 (m-80) cc_final: 0.8724 (m-80) REVERT: A 392 ASN cc_start: 0.9262 (m-40) cc_final: 0.8927 (m-40) REVERT: A 394 PHE cc_start: 0.8244 (t80) cc_final: 0.7676 (t80) REVERT: A 397 PHE cc_start: 0.7785 (t80) cc_final: 0.7329 (t80) REVERT: A 414 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 432 MET cc_start: 0.8203 (tpt) cc_final: 0.7870 (tpt) REVERT: A 433 VAL cc_start: 0.8898 (p) cc_final: 0.8686 (m) REVERT: A 443 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 454 VAL cc_start: 0.9024 (t) cc_final: 0.8779 (t) REVERT: A 458 LEU cc_start: 0.8737 (mt) cc_final: 0.8469 (mt) REVERT: A 459 LYS cc_start: 0.8398 (tppp) cc_final: 0.6502 (tppp) REVERT: A 463 MET cc_start: 0.7953 (mmp) cc_final: 0.6887 (mmp) REVERT: A 467 ASP cc_start: 0.7943 (p0) cc_final: 0.7688 (p0) REVERT: A 470 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7406 (ptt-90) REVERT: A 472 TRP cc_start: 0.8500 (t-100) cc_final: 0.7819 (t-100) REVERT: A 473 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8598 (pttp) REVERT: A 486 CYS cc_start: 0.8807 (t) cc_final: 0.8270 (p) REVERT: A 487 ILE cc_start: 0.9002 (mt) cc_final: 0.8662 (pt) REVERT: A 496 LEU cc_start: 0.9015 (tp) cc_final: 0.8691 (tp) REVERT: A 514 GLN cc_start: 0.8313 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 530 TYR cc_start: 0.8201 (m-10) cc_final: 0.7959 (m-10) REVERT: A 535 HIS cc_start: 0.7182 (m90) cc_final: 0.6764 (m-70) REVERT: A 536 TYR cc_start: 0.8294 (m-80) cc_final: 0.8041 (m-80) REVERT: A 540 GLU cc_start: 0.7667 (pt0) cc_final: 0.7092 (pm20) REVERT: A 549 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7272 (tpp-160) REVERT: A 560 ASP cc_start: 0.8433 (m-30) cc_final: 0.8183 (t0) REVERT: A 563 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8290 (mmmt) REVERT: A 564 LYS cc_start: 0.8943 (tppt) cc_final: 0.8418 (tppt) REVERT: A 580 LYS cc_start: 0.7774 (tttt) cc_final: 0.7345 (tttp) REVERT: A 590 LYS cc_start: 0.8564 (pptt) cc_final: 0.8249 (tmmt) REVERT: A 677 ARG cc_start: 0.8387 (ttt180) cc_final: 0.7864 (tpp80) REVERT: A 687 ASP cc_start: 0.8542 (t0) cc_final: 0.8124 (t0) REVERT: A 697 ASP cc_start: 0.8561 (m-30) cc_final: 0.8329 (p0) REVERT: A 705 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7673 (tp-100) REVERT: A 724 ASP cc_start: 0.8473 (m-30) cc_final: 0.8155 (m-30) REVERT: A 727 LEU cc_start: 0.8790 (mm) cc_final: 0.8310 (mm) REVERT: A 728 HIS cc_start: 0.8843 (t70) cc_final: 0.8582 (t70) REVERT: A 731 ASN cc_start: 0.8513 (m110) cc_final: 0.8156 (m110) REVERT: B 27 TYR cc_start: 0.8835 (m-10) cc_final: 0.8240 (m-10) REVERT: B 33 GLN cc_start: 0.8338 (pp30) cc_final: 0.7966 (pp30) REVERT: B 100 LEU cc_start: 0.7932 (tp) cc_final: 0.7582 (tp) REVERT: B 105 TYR cc_start: 0.7384 (m-80) cc_final: 0.7085 (m-80) REVERT: B 122 PHE cc_start: 0.8295 (m-80) cc_final: 0.7761 (m-80) REVERT: B 124 ILE cc_start: 0.8834 (mm) cc_final: 0.8434 (pt) REVERT: B 125 LEU cc_start: 0.8825 (mt) cc_final: 0.8514 (mt) REVERT: B 137 SER cc_start: 0.8051 (t) cc_final: 0.7728 (t) REVERT: B 147 MET cc_start: 0.9026 (mtt) cc_final: 0.8670 (mmp) REVERT: B 186 VAL cc_start: 0.8967 (p) cc_final: 0.8667 (m) REVERT: B 199 ILE cc_start: 0.8511 (tp) cc_final: 0.7870 (pt) REVERT: B 207 GLN cc_start: 0.8871 (tt0) cc_final: 0.8410 (tm-30) REVERT: B 230 GLN cc_start: 0.8471 (pp30) cc_final: 0.7893 (pp30) REVERT: B 236 LEU cc_start: 0.8737 (tp) cc_final: 0.8480 (tp) REVERT: B 237 LYS cc_start: 0.8978 (pttt) cc_final: 0.8487 (pttp) REVERT: B 238 ILE cc_start: 0.8664 (tp) cc_final: 0.8275 (pt) REVERT: B 241 ASN cc_start: 0.7967 (m110) cc_final: 0.7362 (m110) REVERT: B 250 ILE cc_start: 0.8670 (pt) cc_final: 0.8343 (mm) REVERT: B 251 LEU cc_start: 0.8566 (mm) cc_final: 0.6666 (mm) REVERT: B 255 TYR cc_start: 0.7693 (m-10) cc_final: 0.7048 (m-80) REVERT: B 260 ILE cc_start: 0.9205 (mm) cc_final: 0.8846 (mt) REVERT: B 271 ASP cc_start: 0.8379 (t0) cc_final: 0.8088 (t0) REVERT: B 286 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8784 (mtmm) REVERT: B 303 GLU cc_start: 0.8981 (mp0) cc_final: 0.8574 (mp0) REVERT: B 318 ASN cc_start: 0.8538 (t0) cc_final: 0.8309 (t0) REVERT: B 319 LEU cc_start: 0.8709 (mt) cc_final: 0.8381 (mt) REVERT: B 321 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8408 (ttpp) REVERT: B 322 ASN cc_start: 0.8095 (m110) cc_final: 0.7483 (t0) REVERT: B 323 TYR cc_start: 0.8206 (m-80) cc_final: 0.7007 (m-80) REVERT: B 440 ARG cc_start: 0.7600 (mmm160) cc_final: 0.6905 (mmm160) REVERT: B 455 ILE cc_start: 0.8694 (mt) cc_final: 0.8219 (mp) REVERT: B 459 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7493 (mmtt) REVERT: B 463 MET cc_start: 0.7222 (mmm) cc_final: 0.6323 (mmm) REVERT: B 473 LYS cc_start: 0.8448 (mttp) cc_final: 0.7697 (pttt) REVERT: B 477 THR cc_start: 0.8103 (m) cc_final: 0.7735 (p) REVERT: B 478 ASP cc_start: 0.8462 (p0) cc_final: 0.8199 (p0) REVERT: B 482 TRP cc_start: 0.8383 (t60) cc_final: 0.8137 (t60) REVERT: B 484 PHE cc_start: 0.8395 (t80) cc_final: 0.7837 (t80) REVERT: B 488 MET cc_start: 0.7716 (tpp) cc_final: 0.6439 (tpp) REVERT: B 491 ILE cc_start: 0.8973 (mt) cc_final: 0.8690 (mm) REVERT: B 492 LEU cc_start: 0.8747 (mt) cc_final: 0.7330 (mt) REVERT: B 496 LEU cc_start: 0.7967 (mt) cc_final: 0.7632 (mm) REVERT: B 512 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8300 (mtm-85) REVERT: B 514 GLN cc_start: 0.8774 (tt0) cc_final: 0.8328 (tm-30) REVERT: B 563 LYS cc_start: 0.8991 (tppt) cc_final: 0.7890 (tppt) REVERT: B 567 ASN cc_start: 0.8235 (m-40) cc_final: 0.7751 (m110) REVERT: B 577 VAL cc_start: 0.9001 (m) cc_final: 0.8740 (p) REVERT: B 578 TYR cc_start: 0.7914 (t80) cc_final: 0.6065 (t80) REVERT: B 674 ARG cc_start: 0.8878 (ttm110) cc_final: 0.8079 (ttm110) REVERT: B 677 ARG cc_start: 0.8569 (ttt180) cc_final: 0.7878 (ttm-80) REVERT: B 678 MET cc_start: 0.8173 (mmm) cc_final: 0.7830 (mmm) REVERT: B 682 GLU cc_start: 0.8286 (tp30) cc_final: 0.7854 (tp30) REVERT: B 685 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7595 (mtm180) REVERT: B 687 ASP cc_start: 0.8199 (t0) cc_final: 0.7903 (t0) REVERT: B 691 TYR cc_start: 0.7615 (m-80) cc_final: 0.6899 (m-80) REVERT: B 701 GLU cc_start: 0.7770 (mp0) cc_final: 0.7558 (mp0) REVERT: B 702 LYS cc_start: 0.7613 (tptp) cc_final: 0.7044 (tptp) REVERT: B 705 GLN cc_start: 0.8580 (tt0) cc_final: 0.8108 (pp30) REVERT: B 719 PHE cc_start: 0.7901 (m-80) cc_final: 0.7636 (m-10) REVERT: B 720 LEU cc_start: 0.9157 (mp) cc_final: 0.8897 (mp) REVERT: B 727 LEU cc_start: 0.8979 (mt) cc_final: 0.8485 (mt) REVERT: B 730 GLN cc_start: 0.8982 (tt0) cc_final: 0.8346 (tm-30) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2843 time to fit residues: 138.0283 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 0.5980 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090852 restraints weight = 26210.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094161 restraints weight = 15955.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096514 restraints weight = 10943.328| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10395 Z= 0.138 Angle : 0.637 9.552 14128 Z= 0.326 Chirality : 0.044 0.313 1716 Planarity : 0.004 0.053 1757 Dihedral : 4.172 22.857 1415 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.23), residues: 1319 helix: 0.40 (0.18), residues: 843 sheet: -1.56 (1.03), residues: 34 loop : -2.47 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 74 HIS 0.003 0.000 HIS A 723 PHE 0.026 0.001 PHE B 261 TYR 0.015 0.001 TYR A 361 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 546) hydrogen bonds : angle 3.86645 ( 1596) covalent geometry : bond 0.00299 (10395) covalent geometry : angle 0.63716 (14128) *********************** 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 368 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.095 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: 0.8489 (t80) cc_final: 0.8203 (t80) REVERT: A 38 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7425 (ttm110) REVERT: A 59 LYS cc_start: 0.8506 (tptt) cc_final: 0.8223 (mmmt) REVERT: A 96 LEU cc_start: 0.8783 (mt) cc_final: 0.8463 (mm) REVERT: A 103 MET cc_start: 0.8405 (mtm) cc_final: 0.7953 (mtm) REVERT: A 105 TYR cc_start: 0.8645 (m-10) cc_final: 0.8395 (m-80) REVERT: A 115 PHE cc_start: 0.8892 (m-80) cc_final: 0.8609 (m-10) REVERT: A 118 TYR cc_start: 0.8287 (m-80) cc_final: 0.7900 (m-80) REVERT: A 119 SER cc_start: 0.8663 (t) cc_final: 0.8195 (p) REVERT: A 121 PHE cc_start: 0.7622 (t80) cc_final: 0.7306 (t80) REVERT: A 194 LEU cc_start: 0.8400 (tp) cc_final: 0.8069 (mm) REVERT: A 211 ILE cc_start: 0.9024 (tt) cc_final: 0.8762 (tp) REVERT: A 230 GLN cc_start: 0.8791 (mt0) cc_final: 0.8215 (tp40) REVERT: A 234 SER cc_start: 0.9193 (m) cc_final: 0.8780 (p) REVERT: A 235 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 237 LYS cc_start: 0.8962 (pttp) cc_final: 0.8474 (pttp) REVERT: A 240 LEU cc_start: 0.8581 (mm) cc_final: 0.8350 (mp) REVERT: A 252 SER cc_start: 0.8246 (p) cc_final: 0.7779 (m) REVERT: A 262 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 272 PHE cc_start: 0.8161 (t80) cc_final: 0.7781 (t80) REVERT: A 276 LEU cc_start: 0.8707 (pp) cc_final: 0.8479 (pp) REVERT: A 279 ILE cc_start: 0.9090 (mm) cc_final: 0.8636 (tp) REVERT: A 281 VAL cc_start: 0.8877 (m) cc_final: 0.8677 (p) REVERT: A 282 CYS cc_start: 0.8724 (t) cc_final: 0.8259 (p) REVERT: A 283 MET cc_start: 0.7605 (mmp) cc_final: 0.7206 (mmp) REVERT: A 286 LYS cc_start: 0.8912 (tppt) cc_final: 0.8604 (tppt) REVERT: A 293 LYS cc_start: 0.8303 (tppt) cc_final: 0.7826 (tppt) REVERT: A 309 ILE cc_start: 0.8929 (tp) cc_final: 0.8654 (pt) REVERT: A 324 ASN cc_start: 0.8215 (t0) cc_final: 0.7894 (t0) REVERT: A 345 LEU cc_start: 0.8485 (mt) cc_final: 0.7843 (pt) REVERT: A 349 MET cc_start: 0.7751 (ptt) cc_final: 0.7109 (ptt) REVERT: A 353 SER cc_start: 0.8908 (m) cc_final: 0.8647 (p) REVERT: A 369 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8618 (tppt) REVERT: A 371 TYR cc_start: 0.8330 (m-80) cc_final: 0.7770 (m-80) REVERT: A 385 PHE cc_start: 0.8012 (t80) cc_final: 0.7361 (t80) REVERT: A 388 PHE cc_start: 0.8951 (m-80) cc_final: 0.8719 (m-80) REVERT: A 392 ASN cc_start: 0.9259 (m-40) cc_final: 0.8909 (m-40) REVERT: A 394 PHE cc_start: 0.8247 (t80) cc_final: 0.7659 (t80) REVERT: A 397 PHE cc_start: 0.7863 (t80) cc_final: 0.7382 (t80) REVERT: A 414 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 432 MET cc_start: 0.8195 (tpt) cc_final: 0.7926 (tpt) REVERT: A 433 VAL cc_start: 0.8901 (p) cc_final: 0.8697 (m) REVERT: A 443 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 454 VAL cc_start: 0.9054 (t) cc_final: 0.8789 (t) REVERT: A 458 LEU cc_start: 0.8839 (mt) cc_final: 0.8532 (mt) REVERT: A 459 LYS cc_start: 0.8446 (tppp) cc_final: 0.6579 (tppp) REVERT: A 463 MET cc_start: 0.7979 (mmp) cc_final: 0.7173 (mmp) REVERT: A 467 ASP cc_start: 0.7912 (p0) cc_final: 0.7656 (p0) REVERT: A 470 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7407 (ptt-90) REVERT: A 472 TRP cc_start: 0.8474 (t-100) cc_final: 0.7764 (t-100) REVERT: A 473 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8604 (pttp) REVERT: A 486 CYS cc_start: 0.8792 (t) cc_final: 0.8262 (p) REVERT: A 487 ILE cc_start: 0.8957 (mt) cc_final: 0.8598 (pt) REVERT: A 496 LEU cc_start: 0.8999 (tp) cc_final: 0.8666 (tp) REVERT: A 514 GLN cc_start: 0.8435 (tt0) cc_final: 0.7906 (tm-30) REVERT: A 535 HIS cc_start: 0.7328 (m90) cc_final: 0.6862 (m-70) REVERT: A 549 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7287 (tpp-160) REVERT: A 560 ASP cc_start: 0.8397 (m-30) cc_final: 0.8171 (t0) REVERT: A 563 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8241 (mmmt) REVERT: A 564 LYS cc_start: 0.8939 (tppt) cc_final: 0.8471 (tppt) REVERT: A 580 LYS cc_start: 0.7776 (tttt) cc_final: 0.7318 (tttp) REVERT: A 590 LYS cc_start: 0.8567 (pptt) cc_final: 0.8233 (tmmt) REVERT: A 677 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7870 (tpp80) REVERT: A 678 MET cc_start: 0.8063 (mmm) cc_final: 0.7785 (mmm) REVERT: A 687 ASP cc_start: 0.8530 (t0) cc_final: 0.8117 (t0) REVERT: A 697 ASP cc_start: 0.8545 (m-30) cc_final: 0.8325 (p0) REVERT: A 703 MET cc_start: 0.7789 (ttm) cc_final: 0.7552 (ttp) REVERT: A 705 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7756 (tm-30) REVERT: A 723 HIS cc_start: 0.8017 (t70) cc_final: 0.7800 (t70) REVERT: A 724 ASP cc_start: 0.8419 (m-30) cc_final: 0.7860 (m-30) REVERT: A 727 LEU cc_start: 0.8738 (mm) cc_final: 0.8144 (mt) REVERT: A 728 HIS cc_start: 0.8855 (t70) cc_final: 0.8580 (t70) REVERT: A 731 ASN cc_start: 0.8482 (m110) cc_final: 0.8124 (m110) REVERT: B 27 TYR cc_start: 0.8822 (m-10) cc_final: 0.8237 (m-10) REVERT: B 33 GLN cc_start: 0.8334 (pp30) cc_final: 0.8012 (pp30) REVERT: B 105 TYR cc_start: 0.7327 (m-80) cc_final: 0.7012 (m-80) REVERT: B 122 PHE cc_start: 0.8320 (m-80) cc_final: 0.7750 (m-80) REVERT: B 124 ILE cc_start: 0.8849 (mm) cc_final: 0.8404 (pt) REVERT: B 125 LEU cc_start: 0.8815 (mt) cc_final: 0.8526 (mt) REVERT: B 137 SER cc_start: 0.8041 (t) cc_final: 0.7717 (t) REVERT: B 147 MET cc_start: 0.9007 (mtt) cc_final: 0.8669 (mmp) REVERT: B 186 VAL cc_start: 0.8966 (p) cc_final: 0.8654 (m) REVERT: B 196 VAL cc_start: 0.9004 (t) cc_final: 0.8624 (t) REVERT: B 199 ILE cc_start: 0.8325 (tp) cc_final: 0.7896 (pt) REVERT: B 207 GLN cc_start: 0.8875 (tt0) cc_final: 0.8411 (tm-30) REVERT: B 230 GLN cc_start: 0.8474 (pp30) cc_final: 0.7893 (pp30) REVERT: B 236 LEU cc_start: 0.8761 (tp) cc_final: 0.8490 (tp) REVERT: B 237 LYS cc_start: 0.8977 (pttt) cc_final: 0.8465 (pttp) REVERT: B 238 ILE cc_start: 0.8678 (tp) cc_final: 0.8270 (pt) REVERT: B 241 ASN cc_start: 0.7923 (m110) cc_final: 0.7167 (m110) REVERT: B 247 TYR cc_start: 0.8221 (m-10) cc_final: 0.7874 (m-10) REVERT: B 250 ILE cc_start: 0.8708 (pt) cc_final: 0.8357 (mm) REVERT: B 251 LEU cc_start: 0.8564 (mm) cc_final: 0.6656 (mm) REVERT: B 255 TYR cc_start: 0.7700 (m-10) cc_final: 0.7101 (m-80) REVERT: B 271 ASP cc_start: 0.8318 (t0) cc_final: 0.7986 (t0) REVERT: B 286 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8783 (mtmm) REVERT: B 303 GLU cc_start: 0.8986 (mp0) cc_final: 0.8577 (mp0) REVERT: B 318 ASN cc_start: 0.8551 (t0) cc_final: 0.8322 (t0) REVERT: B 319 LEU cc_start: 0.8721 (mt) cc_final: 0.8376 (mt) REVERT: B 321 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8377 (ttpp) REVERT: B 322 ASN cc_start: 0.8122 (m110) cc_final: 0.7558 (t0) REVERT: B 323 TYR cc_start: 0.8226 (m-80) cc_final: 0.7023 (m-80) REVERT: B 349 MET cc_start: 0.6716 (tmm) cc_final: 0.6307 (ppp) REVERT: B 440 ARG cc_start: 0.7604 (mmm160) cc_final: 0.6923 (mmm160) REVERT: B 447 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8147 (ptpp) REVERT: B 455 ILE cc_start: 0.8676 (mt) cc_final: 0.8092 (mp) REVERT: B 459 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7481 (mmtt) REVERT: B 461 MET cc_start: 0.8611 (mtp) cc_final: 0.8355 (mtp) REVERT: B 463 MET cc_start: 0.7279 (mmm) cc_final: 0.6363 (mmm) REVERT: B 473 LYS cc_start: 0.8493 (mttp) cc_final: 0.7550 (pttm) REVERT: B 476 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8030 (mmmm) REVERT: B 477 THR cc_start: 0.8329 (m) cc_final: 0.8069 (p) REVERT: B 484 PHE cc_start: 0.8394 (t80) cc_final: 0.7845 (t80) REVERT: B 488 MET cc_start: 0.7723 (tpp) cc_final: 0.6519 (tpp) REVERT: B 491 ILE cc_start: 0.8992 (mt) cc_final: 0.8712 (mm) REVERT: B 492 LEU cc_start: 0.8737 (mt) cc_final: 0.7406 (mt) REVERT: B 496 LEU cc_start: 0.7935 (mt) cc_final: 0.7704 (mt) REVERT: B 512 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8273 (mtm-85) REVERT: B 514 GLN cc_start: 0.8780 (tt0) cc_final: 0.8352 (tm-30) REVERT: B 529 ILE cc_start: 0.8725 (mm) cc_final: 0.8506 (mp) REVERT: B 563 LYS cc_start: 0.8980 (tppt) cc_final: 0.7833 (tppt) REVERT: B 567 ASN cc_start: 0.8219 (m-40) cc_final: 0.7583 (m110) REVERT: B 577 VAL cc_start: 0.9002 (m) cc_final: 0.8735 (p) REVERT: B 578 TYR cc_start: 0.7859 (t80) cc_final: 0.6259 (t80) REVERT: B 666 SER cc_start: 0.8812 (p) cc_final: 0.8601 (p) REVERT: B 674 ARG cc_start: 0.8886 (ttm110) cc_final: 0.8110 (ttm110) REVERT: B 677 ARG cc_start: 0.8583 (ttt180) cc_final: 0.7864 (ttm-80) REVERT: B 678 MET cc_start: 0.8185 (mmm) cc_final: 0.7854 (mmm) REVERT: B 682 GLU cc_start: 0.8283 (tp30) cc_final: 0.7848 (tp30) REVERT: B 685 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7618 (mtm180) REVERT: B 691 TYR cc_start: 0.7616 (m-80) cc_final: 0.6903 (m-80) REVERT: B 701 GLU cc_start: 0.7832 (mp0) cc_final: 0.7587 (mp0) REVERT: B 702 LYS cc_start: 0.7718 (tptp) cc_final: 0.7319 (tptp) REVERT: B 705 GLN cc_start: 0.8562 (tt0) cc_final: 0.8083 (pp30) REVERT: B 716 ASP cc_start: 0.8316 (p0) cc_final: 0.7396 (t0) REVERT: B 720 LEU cc_start: 0.9198 (mp) cc_final: 0.8931 (mp) REVERT: B 727 LEU cc_start: 0.8978 (mt) cc_final: 0.8454 (mt) REVERT: B 730 GLN cc_start: 0.8987 (tt0) cc_final: 0.8325 (tm-30) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2909 time to fit residues: 140.0009 Evaluate side-chains 342 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 0.9980 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089611 restraints weight = 26402.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092916 restraints weight = 16023.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095302 restraints weight = 10898.774| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5389 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= 0.165 Angle : 0.657 9.601 14128 Z= 0.340 Chirality : 0.045 0.332 1716 Planarity : 0.004 0.053 1757 Dihedral : 4.286 21.958 1415 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: -0.90 (0.23), residues: 1319 helix: 0.34 (0.18), residues: 841 sheet: -1.59 (1.02), residues: 34 loop : -2.33 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 482 HIS 0.003 0.001 HIS A 723 PHE 0.031 0.002 PHE B 203 TYR 0.017 0.001 TYR B 377 ARG 0.008 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 546) hydrogen bonds : angle 3.91733 ( 1596) covalent geometry : bond 0.00340 (10395) covalent geometry : angle 0.65734 (14128) *********************** 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 364 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.075 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: 0.8518 (t80) cc_final: 0.8241 (t80) REVERT: A 29 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 38 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7525 (ttm110) REVERT: A 96 LEU cc_start: 0.8777 (mt) cc_final: 0.8470 (mm) REVERT: A 103 MET cc_start: 0.8482 (mtm) cc_final: 0.7897 (mtm) REVERT: A 105 TYR cc_start: 0.8521 (m-10) cc_final: 0.8248 (m-80) REVERT: A 119 SER cc_start: 0.8649 (t) cc_final: 0.8226 (p) REVERT: A 121 PHE cc_start: 0.7715 (t80) cc_final: 0.7357 (t80) REVERT: A 185 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8294 (ttp-110) REVERT: A 194 LEU cc_start: 0.8418 (tp) cc_final: 0.8072 (mm) REVERT: A 211 ILE cc_start: 0.9042 (tt) cc_final: 0.8780 (tp) REVERT: A 230 GLN cc_start: 0.8816 (mt0) cc_final: 0.8235 (tp40) REVERT: A 234 SER cc_start: 0.9197 (m) cc_final: 0.8723 (p) REVERT: A 235 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 237 LYS cc_start: 0.8982 (pttp) cc_final: 0.8431 (pttp) REVERT: A 240 LEU cc_start: 0.8584 (mm) cc_final: 0.8368 (mp) REVERT: A 252 SER cc_start: 0.8301 (p) cc_final: 0.7831 (m) REVERT: A 262 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 272 PHE cc_start: 0.8167 (t80) cc_final: 0.7801 (t80) REVERT: A 276 LEU cc_start: 0.8719 (pp) cc_final: 0.8491 (pp) REVERT: A 279 ILE cc_start: 0.9075 (mm) cc_final: 0.8641 (tp) REVERT: A 281 VAL cc_start: 0.8905 (m) cc_final: 0.8701 (p) REVERT: A 282 CYS cc_start: 0.8703 (t) cc_final: 0.8279 (p) REVERT: A 283 MET cc_start: 0.7600 (mmp) cc_final: 0.7309 (mmp) REVERT: A 286 LYS cc_start: 0.8916 (tppt) cc_final: 0.8522 (tppt) REVERT: A 293 LYS cc_start: 0.8253 (tppt) cc_final: 0.7760 (tppt) REVERT: A 305 ILE cc_start: 0.8723 (tp) cc_final: 0.8270 (pt) REVERT: A 309 ILE cc_start: 0.8938 (tp) cc_final: 0.8647 (pt) REVERT: A 324 ASN cc_start: 0.8250 (t0) cc_final: 0.7916 (t0) REVERT: A 345 LEU cc_start: 0.8432 (mt) cc_final: 0.7901 (pt) REVERT: A 349 MET cc_start: 0.7744 (ptt) cc_final: 0.7091 (ptt) REVERT: A 353 SER cc_start: 0.8942 (m) cc_final: 0.8679 (p) REVERT: A 369 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8641 (tppt) REVERT: A 371 TYR cc_start: 0.8365 (m-80) cc_final: 0.7776 (m-80) REVERT: A 385 PHE cc_start: 0.8023 (t80) cc_final: 0.7377 (t80) REVERT: A 388 PHE cc_start: 0.8943 (m-80) cc_final: 0.8710 (m-80) REVERT: A 392 ASN cc_start: 0.9271 (m-40) cc_final: 0.8924 (m-40) REVERT: A 394 PHE cc_start: 0.8277 (t80) cc_final: 0.7699 (t80) REVERT: A 397 PHE cc_start: 0.7909 (t80) cc_final: 0.7399 (t80) REVERT: A 414 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 432 MET cc_start: 0.8199 (tpt) cc_final: 0.7958 (tpt) REVERT: A 443 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 454 VAL cc_start: 0.9086 (t) cc_final: 0.8817 (t) REVERT: A 458 LEU cc_start: 0.8728 (mt) cc_final: 0.8466 (mt) REVERT: A 459 LYS cc_start: 0.8421 (tppp) cc_final: 0.6614 (tppp) REVERT: A 461 MET cc_start: 0.8892 (mtm) cc_final: 0.8590 (ptp) REVERT: A 463 MET cc_start: 0.8026 (mmp) cc_final: 0.7080 (mmp) REVERT: A 467 ASP cc_start: 0.7978 (p0) cc_final: 0.7706 (p0) REVERT: A 470 ARG cc_start: 0.7984 (ptp-170) cc_final: 0.7435 (ptt-90) REVERT: A 472 TRP cc_start: 0.8527 (t-100) cc_final: 0.7819 (t-100) REVERT: A 473 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8609 (pttp) REVERT: A 486 CYS cc_start: 0.8834 (t) cc_final: 0.8279 (p) REVERT: A 487 ILE cc_start: 0.9018 (mt) cc_final: 0.8676 (pt) REVERT: A 496 LEU cc_start: 0.9009 (tp) cc_final: 0.8467 (tp) REVERT: A 514 GLN cc_start: 0.8422 (tt0) cc_final: 0.7885 (tm-30) REVERT: A 540 GLU cc_start: 0.7665 (pt0) cc_final: 0.7036 (pm20) REVERT: A 549 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7170 (tpp-160) REVERT: A 563 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8316 (mmmt) REVERT: A 564 LYS cc_start: 0.8992 (tppt) cc_final: 0.8429 (tppt) REVERT: A 590 LYS cc_start: 0.8587 (pptt) cc_final: 0.8240 (tmmt) REVERT: A 677 ARG cc_start: 0.8385 (ttt180) cc_final: 0.7852 (tpp80) REVERT: A 687 ASP cc_start: 0.8534 (t0) cc_final: 0.8123 (t0) REVERT: A 705 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7787 (tm-30) REVERT: A 723 HIS cc_start: 0.8089 (t70) cc_final: 0.7647 (t70) REVERT: A 724 ASP cc_start: 0.8314 (m-30) cc_final: 0.7786 (m-30) REVERT: A 727 LEU cc_start: 0.8751 (mm) cc_final: 0.8092 (mt) REVERT: A 728 HIS cc_start: 0.8870 (t70) cc_final: 0.8443 (t-90) REVERT: A 731 ASN cc_start: 0.8496 (m110) cc_final: 0.8151 (m110) REVERT: B 27 TYR cc_start: 0.8900 (m-10) cc_final: 0.8346 (m-10) REVERT: B 33 GLN cc_start: 0.8331 (pp30) cc_final: 0.7998 (pp30) REVERT: B 105 TYR cc_start: 0.7319 (m-80) cc_final: 0.7033 (m-80) REVERT: B 122 PHE cc_start: 0.8339 (m-80) cc_final: 0.7803 (m-80) REVERT: B 124 ILE cc_start: 0.8861 (mm) cc_final: 0.8434 (pt) REVERT: B 125 LEU cc_start: 0.8840 (mt) cc_final: 0.8548 (mt) REVERT: B 137 SER cc_start: 0.8054 (t) cc_final: 0.7714 (t) REVERT: B 147 MET cc_start: 0.9024 (mtt) cc_final: 0.8707 (mmp) REVERT: B 186 VAL cc_start: 0.8926 (p) cc_final: 0.8614 (m) REVERT: B 199 ILE cc_start: 0.8447 (tp) cc_final: 0.7941 (pt) REVERT: B 203 PHE cc_start: 0.6738 (m-80) cc_final: 0.6433 (m-80) REVERT: B 207 GLN cc_start: 0.8901 (tt0) cc_final: 0.8415 (tm-30) REVERT: B 230 GLN cc_start: 0.8503 (pp30) cc_final: 0.7929 (pp30) REVERT: B 236 LEU cc_start: 0.8772 (tp) cc_final: 0.8447 (tp) REVERT: B 237 LYS cc_start: 0.9000 (pttt) cc_final: 0.8477 (pttp) REVERT: B 238 ILE cc_start: 0.8687 (tp) cc_final: 0.8278 (pt) REVERT: B 240 LEU cc_start: 0.9052 (mm) cc_final: 0.8850 (mm) REVERT: B 241 ASN cc_start: 0.7895 (m110) cc_final: 0.7389 (m110) REVERT: B 247 TYR cc_start: 0.8308 (m-10) cc_final: 0.7871 (m-10) REVERT: B 250 ILE cc_start: 0.8686 (pt) cc_final: 0.8368 (mm) REVERT: B 251 LEU cc_start: 0.8578 (mm) cc_final: 0.6671 (mm) REVERT: B 255 TYR cc_start: 0.7741 (m-10) cc_final: 0.7156 (m-80) REVERT: B 286 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8759 (mtmm) REVERT: B 290 ASP cc_start: 0.8396 (m-30) cc_final: 0.8165 (m-30) REVERT: B 303 GLU cc_start: 0.8995 (mp0) cc_final: 0.8580 (mp0) REVERT: B 318 ASN cc_start: 0.8539 (t0) cc_final: 0.8280 (t0) REVERT: B 319 LEU cc_start: 0.8730 (mt) cc_final: 0.8379 (mt) REVERT: B 321 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8387 (ttpp) REVERT: B 322 ASN cc_start: 0.8099 (m110) cc_final: 0.7512 (t0) REVERT: B 323 TYR cc_start: 0.8259 (m-80) cc_final: 0.7070 (m-80) REVERT: B 349 MET cc_start: 0.6798 (tmm) cc_final: 0.6471 (ppp) REVERT: B 440 ARG cc_start: 0.7672 (mmm160) cc_final: 0.6962 (mmm160) REVERT: B 447 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8380 (ptpp) REVERT: B 455 ILE cc_start: 0.8768 (mt) cc_final: 0.8184 (mm) REVERT: B 459 LYS cc_start: 0.8661 (mmtt) cc_final: 0.7470 (mmtt) REVERT: B 463 MET cc_start: 0.7273 (mmm) cc_final: 0.6347 (mmm) REVERT: B 473 LYS cc_start: 0.8475 (mttp) cc_final: 0.7594 (pttt) REVERT: B 476 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8026 (mmmm) REVERT: B 477 THR cc_start: 0.8332 (m) cc_final: 0.8100 (p) REVERT: B 484 PHE cc_start: 0.8407 (t80) cc_final: 0.7825 (t80) REVERT: B 488 MET cc_start: 0.7749 (tpp) cc_final: 0.6550 (tpp) REVERT: B 491 ILE cc_start: 0.9003 (mt) cc_final: 0.8720 (mm) REVERT: B 492 LEU cc_start: 0.8750 (mt) cc_final: 0.7393 (mt) REVERT: B 496 LEU cc_start: 0.7928 (mt) cc_final: 0.7696 (mt) REVERT: B 512 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8251 (mtm-85) REVERT: B 514 GLN cc_start: 0.8786 (tt0) cc_final: 0.8350 (tm-30) REVERT: B 563 LYS cc_start: 0.8981 (tppt) cc_final: 0.7850 (tppt) REVERT: B 567 ASN cc_start: 0.8229 (m-40) cc_final: 0.7608 (m110) REVERT: B 577 VAL cc_start: 0.8993 (m) cc_final: 0.8738 (p) REVERT: B 578 TYR cc_start: 0.7863 (t80) cc_final: 0.6253 (t80) REVERT: B 674 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8160 (ttm110) REVERT: B 677 ARG cc_start: 0.8548 (ttt180) cc_final: 0.8071 (ttm-80) REVERT: B 678 MET cc_start: 0.8169 (mmm) cc_final: 0.7870 (mmm) REVERT: B 682 GLU cc_start: 0.8274 (tp30) cc_final: 0.7841 (tp30) REVERT: B 685 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7576 (mtm180) REVERT: B 701 GLU cc_start: 0.7697 (mp0) cc_final: 0.7431 (mp0) REVERT: B 702 LYS cc_start: 0.7814 (tptp) cc_final: 0.7354 (tptp) REVERT: B 705 GLN cc_start: 0.8534 (tt0) cc_final: 0.8068 (pp30) REVERT: B 716 ASP cc_start: 0.8298 (p0) cc_final: 0.7550 (t0) REVERT: B 720 LEU cc_start: 0.9191 (mp) cc_final: 0.8875 (mp) REVERT: B 727 LEU cc_start: 0.8924 (mt) cc_final: 0.8443 (mt) REVERT: B 730 GLN cc_start: 0.8960 (tt0) cc_final: 0.8366 (pp30) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2935 time to fit residues: 141.7768 Evaluate side-chains 334 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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: 0.4980 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS B 375 HIS B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.112625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090800 restraints weight = 26483.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094106 restraints weight = 15952.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096435 restraints weight = 10808.427| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5514 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= 0.143 Angle : 0.656 10.650 14128 Z= 0.335 Chirality : 0.044 0.331 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.293 22.250 1415 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1319 helix: 0.41 (0.18), residues: 840 sheet: -1.44 (1.00), residues: 36 loop : -2.37 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 482 HIS 0.006 0.001 HIS A 723 PHE 0.030 0.001 PHE B 203 TYR 0.032 0.002 TYR A 361 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 546) hydrogen bonds : angle 3.92538 ( 1596) covalent geometry : bond 0.00311 (10395) covalent geometry : angle 0.65598 (14128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.155 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 20 TYR cc_start: 0.8513 (t80) cc_final: 0.8258 (t80) REVERT: A 29 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 38 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7484 (ttm110) REVERT: A 96 LEU cc_start: 0.8812 (mt) cc_final: 0.8478 (mm) REVERT: A 99 THR cc_start: 0.8997 (t) cc_final: 0.8243 (t) REVERT: A 105 TYR cc_start: 0.8498 (m-10) cc_final: 0.8247 (m-80) REVERT: A 115 PHE cc_start: 0.8895 (m-10) cc_final: 0.8437 (m-10) REVERT: A 118 TYR cc_start: 0.8309 (m-80) cc_final: 0.7965 (m-80) REVERT: A 119 SER cc_start: 0.8687 (t) cc_final: 0.8283 (p) REVERT: A 121 PHE cc_start: 0.7703 (t80) cc_final: 0.7356 (t80) REVERT: A 161 PHE cc_start: 0.7815 (m-10) cc_final: 0.6771 (m-10) REVERT: A 185 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8249 (ttp-110) REVERT: A 194 LEU cc_start: 0.8448 (tp) cc_final: 0.8106 (mm) REVERT: A 211 ILE cc_start: 0.8997 (tt) cc_final: 0.8697 (tp) REVERT: A 213 ARG cc_start: 0.7346 (mtm180) cc_final: 0.7128 (mtt-85) REVERT: A 230 GLN cc_start: 0.8809 (mt0) cc_final: 0.8254 (tp-100) REVERT: A 235 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8246 (mm-40) REVERT: A 237 LYS cc_start: 0.8970 (pttp) cc_final: 0.8513 (pttm) REVERT: A 240 LEU cc_start: 0.8522 (mm) cc_final: 0.8295 (mp) REVERT: A 252 SER cc_start: 0.8296 (p) cc_final: 0.7817 (m) REVERT: A 262 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 272 PHE cc_start: 0.8192 (t80) cc_final: 0.7815 (t80) REVERT: A 276 LEU cc_start: 0.8698 (pp) cc_final: 0.8383 (pp) REVERT: A 279 ILE cc_start: 0.9072 (mm) cc_final: 0.8735 (mm) REVERT: A 281 VAL cc_start: 0.8898 (m) cc_final: 0.8687 (p) REVERT: A 282 CYS cc_start: 0.8718 (t) cc_final: 0.8252 (p) REVERT: A 283 MET cc_start: 0.7586 (mmp) cc_final: 0.7311 (mmp) REVERT: A 286 LYS cc_start: 0.8913 (tppt) cc_final: 0.8586 (tppt) REVERT: A 293 LYS cc_start: 0.8224 (tppt) cc_final: 0.7754 (tppt) REVERT: A 305 ILE cc_start: 0.8715 (tp) cc_final: 0.8507 (tp) REVERT: A 309 ILE cc_start: 0.8935 (tp) cc_final: 0.8653 (pt) REVERT: A 324 ASN cc_start: 0.8233 (t0) cc_final: 0.7907 (t0) REVERT: A 345 LEU cc_start: 0.8380 (mt) cc_final: 0.7787 (pt) REVERT: A 349 MET cc_start: 0.7737 (ptt) cc_final: 0.7105 (ptt) REVERT: A 353 SER cc_start: 0.8971 (m) cc_final: 0.8678 (p) REVERT: A 369 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8608 (tppt) REVERT: A 371 TYR cc_start: 0.8343 (m-80) cc_final: 0.7755 (m-80) REVERT: A 385 PHE cc_start: 0.7949 (t80) cc_final: 0.7384 (t80) REVERT: A 388 PHE cc_start: 0.8938 (m-80) cc_final: 0.8659 (m-80) REVERT: A 392 ASN cc_start: 0.9257 (m-40) cc_final: 0.8918 (m-40) REVERT: A 394 PHE cc_start: 0.8237 (t80) cc_final: 0.7661 (t80) REVERT: A 397 PHE cc_start: 0.7896 (t80) cc_final: 0.7388 (t80) REVERT: A 414 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 432 MET cc_start: 0.8192 (tpt) cc_final: 0.7935 (tpt) REVERT: A 443 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 447 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8939 (mtmt) REVERT: A 454 VAL cc_start: 0.9087 (t) cc_final: 0.8803 (t) REVERT: A 458 LEU cc_start: 0.8880 (mt) cc_final: 0.8509 (mt) REVERT: A 459 LYS cc_start: 0.8430 (tppp) cc_final: 0.6631 (tppp) REVERT: A 461 MET cc_start: 0.8907 (mtm) cc_final: 0.8607 (ptp) REVERT: A 463 MET cc_start: 0.7993 (mmp) cc_final: 0.7191 (mmp) REVERT: A 467 ASP cc_start: 0.7958 (p0) cc_final: 0.7645 (p0) REVERT: A 470 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.7383 (ptt-90) REVERT: A 472 TRP cc_start: 0.8532 (t-100) cc_final: 0.7839 (t-100) REVERT: A 473 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8581 (pttp) REVERT: A 486 CYS cc_start: 0.8805 (t) cc_final: 0.8271 (p) REVERT: A 487 ILE cc_start: 0.8933 (mt) cc_final: 0.8586 (pt) REVERT: A 496 LEU cc_start: 0.8922 (tp) cc_final: 0.8485 (tp) REVERT: A 514 GLN cc_start: 0.8432 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 540 GLU cc_start: 0.7630 (pt0) cc_final: 0.6931 (pm20) REVERT: A 549 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7009 (ttm-80) REVERT: A 563 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8259 (mmmt) REVERT: A 564 LYS cc_start: 0.8958 (tppt) cc_final: 0.8424 (tppt) REVERT: A 590 LYS cc_start: 0.8585 (pptt) cc_final: 0.8233 (tmmt) REVERT: A 677 ARG cc_start: 0.8355 (ttt180) cc_final: 0.7818 (tpp80) REVERT: A 678 MET cc_start: 0.8100 (mmm) cc_final: 0.7809 (mmm) REVERT: A 687 ASP cc_start: 0.8479 (t0) cc_final: 0.8064 (t0) REVERT: A 705 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7679 (tp-100) REVERT: A 724 ASP cc_start: 0.8494 (m-30) cc_final: 0.7946 (m-30) REVERT: A 727 LEU cc_start: 0.8718 (mm) cc_final: 0.8223 (mm) REVERT: A 728 HIS cc_start: 0.8869 (t70) cc_final: 0.8446 (t-90) REVERT: A 731 ASN cc_start: 0.8482 (m110) cc_final: 0.8121 (m110) REVERT: B 27 TYR cc_start: 0.8885 (m-10) cc_final: 0.8317 (m-10) REVERT: B 33 GLN cc_start: 0.8323 (pp30) cc_final: 0.7999 (pp30) REVERT: B 105 TYR cc_start: 0.7234 (m-80) cc_final: 0.6957 (m-80) REVERT: B 122 PHE cc_start: 0.8278 (m-80) cc_final: 0.7769 (m-80) REVERT: B 124 ILE cc_start: 0.8869 (mm) cc_final: 0.8436 (tp) REVERT: B 125 LEU cc_start: 0.8831 (mt) cc_final: 0.8603 (mt) REVERT: B 137 SER cc_start: 0.8064 (t) cc_final: 0.7751 (t) REVERT: B 147 MET cc_start: 0.9009 (mtt) cc_final: 0.8681 (mmp) REVERT: B 186 VAL cc_start: 0.8918 (p) cc_final: 0.8608 (m) REVERT: B 199 ILE cc_start: 0.8446 (tp) cc_final: 0.7919 (pt) REVERT: B 203 PHE cc_start: 0.6717 (m-80) cc_final: 0.6345 (m-80) REVERT: B 207 GLN cc_start: 0.8868 (tt0) cc_final: 0.8374 (tm-30) REVERT: B 230 GLN cc_start: 0.8492 (pp30) cc_final: 0.7869 (pp30) REVERT: B 236 LEU cc_start: 0.8770 (tp) cc_final: 0.8448 (tt) REVERT: B 237 LYS cc_start: 0.9005 (pttt) cc_final: 0.8455 (pttp) REVERT: B 238 ILE cc_start: 0.8663 (tp) cc_final: 0.8254 (pt) REVERT: B 241 ASN cc_start: 0.7902 (m110) cc_final: 0.7292 (m110) REVERT: B 247 TYR cc_start: 0.8238 (m-10) cc_final: 0.7815 (m-10) REVERT: B 250 ILE cc_start: 0.8657 (pt) cc_final: 0.8363 (mm) REVERT: B 251 LEU cc_start: 0.8595 (mm) cc_final: 0.6667 (mm) REVERT: B 255 TYR cc_start: 0.7694 (m-10) cc_final: 0.7103 (m-80) REVERT: B 271 ASP cc_start: 0.8209 (t0) cc_final: 0.7986 (t0) REVERT: B 286 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8850 (mtmm) REVERT: B 303 GLU cc_start: 0.9005 (mp0) cc_final: 0.8581 (mp0) REVERT: B 318 ASN cc_start: 0.8549 (t0) cc_final: 0.8292 (t0) REVERT: B 319 LEU cc_start: 0.8733 (mt) cc_final: 0.8383 (mt) REVERT: B 321 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8382 (ttpp) REVERT: B 322 ASN cc_start: 0.8126 (m110) cc_final: 0.7527 (t0) REVERT: B 323 TYR cc_start: 0.8267 (m-80) cc_final: 0.7126 (m-80) REVERT: B 349 MET cc_start: 0.6714 (tmm) cc_final: 0.6412 (ppp) REVERT: B 440 ARG cc_start: 0.7647 (mmm160) cc_final: 0.6922 (mmm160) REVERT: B 447 LYS cc_start: 0.8755 (ptpt) cc_final: 0.8118 (ptpp) REVERT: B 455 ILE cc_start: 0.8742 (mt) cc_final: 0.8154 (mp) REVERT: B 459 LYS cc_start: 0.8651 (mmtt) cc_final: 0.7475 (mmtt) REVERT: B 461 MET cc_start: 0.8634 (mtp) cc_final: 0.8203 (ptp) REVERT: B 463 MET cc_start: 0.7247 (mmm) cc_final: 0.6337 (mmm) REVERT: B 473 LYS cc_start: 0.8413 (mttp) cc_final: 0.7615 (pttt) REVERT: B 476 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8043 (mmmm) REVERT: B 477 THR cc_start: 0.8299 (m) cc_final: 0.8032 (p) REVERT: B 484 PHE cc_start: 0.8451 (t80) cc_final: 0.7845 (t80) REVERT: B 488 MET cc_start: 0.7708 (tpp) cc_final: 0.6534 (tpp) REVERT: B 491 ILE cc_start: 0.8992 (mt) cc_final: 0.8714 (mm) REVERT: B 492 LEU cc_start: 0.8766 (mt) cc_final: 0.7391 (mt) REVERT: B 496 LEU cc_start: 0.7894 (mt) cc_final: 0.7577 (mm) REVERT: B 512 ARG cc_start: 0.8563 (mtm180) cc_final: 0.8266 (mtm-85) REVERT: B 514 GLN cc_start: 0.8790 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 546 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8447 (mmtm) REVERT: B 563 LYS cc_start: 0.8954 (tppt) cc_final: 0.7863 (tppt) REVERT: B 567 ASN cc_start: 0.8227 (m-40) cc_final: 0.7568 (m110) REVERT: B 576 ARG cc_start: 0.8355 (ptt90) cc_final: 0.8084 (ptt90) REVERT: B 577 VAL cc_start: 0.9001 (m) cc_final: 0.8723 (p) REVERT: B 578 TYR cc_start: 0.7814 (t80) cc_final: 0.6109 (t80) REVERT: B 674 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8105 (ttm110) REVERT: B 677 ARG cc_start: 0.8536 (ttt180) cc_final: 0.7883 (ttm-80) REVERT: B 678 MET cc_start: 0.8136 (mmm) cc_final: 0.7855 (mmm) REVERT: B 685 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7665 (mtm180) REVERT: B 691 TYR cc_start: 0.7613 (m-80) cc_final: 0.6890 (m-80) REVERT: B 702 LYS cc_start: 0.7890 (tptp) cc_final: 0.7321 (tptp) REVERT: B 705 GLN cc_start: 0.8480 (tt0) cc_final: 0.8049 (pp30) REVERT: B 716 ASP cc_start: 0.8317 (p0) cc_final: 0.7480 (t0) REVERT: B 720 LEU cc_start: 0.9201 (mp) cc_final: 0.8884 (mp) REVERT: B 727 LEU cc_start: 0.8945 (mt) cc_final: 0.8478 (mt) REVERT: B 730 GLN cc_start: 0.8914 (tt0) cc_final: 0.8344 (pp30) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2840 time to fit residues: 134.2080 Evaluate side-chains 352 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 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 = 0.3728 r_free = 0.3728 target = 0.111963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090178 restraints weight = 26392.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093495 restraints weight = 15931.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095917 restraints weight = 10816.595| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10395 Z= 0.155 Angle : 0.676 10.196 14128 Z= 0.347 Chirality : 0.045 0.327 1716 Planarity : 0.004 0.052 1757 Dihedral : 4.367 22.036 1415 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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: -0.73 (0.23), residues: 1319 helix: 0.44 (0.18), residues: 831 sheet: -1.45 (0.98), residues: 36 loop : -2.13 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 482 HIS 0.016 0.002 HIS A 723 PHE 0.028 0.002 PHE B 32 TYR 0.045 0.002 TYR A 361 ARG 0.010 0.001 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 546) hydrogen bonds : angle 4.03961 ( 1596) covalent geometry : bond 0.00332 (10395) covalent geometry : angle 0.67614 (14128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.15 seconds wall clock time: 74 minutes 3.54 seconds (4443.54 seconds total)