Starting phenix.real_space_refine on Fri Mar 15 00:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_32580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_32580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_32580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_32580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlb_32580/03_2024/7wlb_32580.pdb" } 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 Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.86, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 4.75 Conformation dependent library (CDL) restraints added in 1.7 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: 1.09 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: 3.19 Time building geometry restraints manager: 5.10 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: 100.80 - 107.45: 297 107.45 - 114.10: 6181 114.10 - 120.74: 4471 120.74 - 127.39: 3105 127.39 - 134.04: 74 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 2.440 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.214 2.440 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 2.440 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.239 2.520 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.284 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.000 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.130 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10395 Z= 0.107 Angle : 0.445 5.533 14128 Z= 0.253 Chirality : 0.037 0.128 1716 Planarity : 0.003 0.042 1757 Dihedral : 8.675 84.585 3714 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.92 % Allowed : 5.70 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.19), residues: 1319 helix: -2.17 (0.15), residues: 815 sheet: -2.99 (0.81), residues: 32 loop : -3.43 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 83 HIS 0.001 0.000 HIS A 656 PHE 0.006 0.001 PHE A 115 TYR 0.005 0.001 TYR A 377 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 402 time to evaluate : 1.070 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: 0.2758 time to fit residues: 156.0042 Evaluate side-chains 361 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 338 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 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: 0.8980 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 268 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 421 GLN A 464 GLN A 567 ASN A 656 HIS 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 474 GLN B 684 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2782 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= 0.227 Angle : 0.612 10.710 14128 Z= 0.318 Chirality : 0.042 0.210 1716 Planarity : 0.004 0.043 1757 Dihedral : 3.388 16.665 1415 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1319 helix: -0.60 (0.17), residues: 835 sheet: -2.21 (0.91), residues: 32 loop : -3.14 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 74 HIS 0.004 0.001 HIS A 723 PHE 0.024 0.001 PHE A 203 TYR 0.010 0.001 TYR B 105 ARG 0.005 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7451 (ttm110) REVERT: A 66 LYS cc_start: 0.8747 (tppt) cc_final: 0.8055 (tppt) REVERT: A 96 LEU cc_start: 0.8910 (mt) cc_final: 0.8549 (pp) REVERT: A 100 LEU cc_start: 0.8833 (mm) cc_final: 0.8536 (mm) REVERT: A 105 TYR cc_start: 0.8500 (m-80) cc_final: 0.8247 (m-80) REVERT: A 115 PHE cc_start: 0.8785 (m-80) cc_final: 0.8490 (m-10) REVERT: A 118 TYR cc_start: 0.7923 (m-10) cc_final: 0.7236 (m-80) REVERT: A 119 SER cc_start: 0.8711 (t) cc_final: 0.7978 (p) REVERT: A 121 PHE cc_start: 0.7715 (t80) cc_final: 0.7410 (t80) REVERT: A 194 LEU cc_start: 0.8558 (tp) cc_final: 0.8290 (mm) REVERT: A 198 ILE cc_start: 0.8607 (mt) cc_final: 0.8349 (tp) REVERT: A 211 ILE cc_start: 0.8730 (tt) cc_final: 0.8517 (tp) REVERT: A 230 GLN cc_start: 0.8849 (mt0) cc_final: 0.8349 (tp-100) REVERT: A 237 LYS cc_start: 0.8891 (pttm) cc_final: 0.8534 (pttm) REVERT: A 251 LEU cc_start: 0.8043 (mt) cc_final: 0.7027 (mm) REVERT: A 252 SER cc_start: 0.8107 (p) cc_final: 0.7612 (m) REVERT: A 255 TYR cc_start: 0.7939 (m-10) cc_final: 0.7576 (m-10) REVERT: A 263 ASN cc_start: 0.8833 (t0) cc_final: 0.8537 (t0) REVERT: A 276 LEU cc_start: 0.8720 (pp) cc_final: 0.8509 (pp) REVERT: A 282 CYS cc_start: 0.8701 (t) cc_final: 0.8279 (p) REVERT: A 286 LYS cc_start: 0.9146 (tppt) cc_final: 0.8554 (tppt) REVERT: A 305 ILE cc_start: 0.8641 (tp) cc_final: 0.8379 (tp) REVERT: A 306 VAL cc_start: 0.8969 (p) cc_final: 0.8645 (m) REVERT: A 309 ILE cc_start: 0.8841 (tp) cc_final: 0.8578 (pt) REVERT: A 315 TYR cc_start: 0.7909 (t80) cc_final: 0.7628 (t80) REVERT: A 321 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8012 (ttpp) REVERT: A 322 ASN cc_start: 0.8172 (m-40) cc_final: 0.7940 (m110) REVERT: A 324 ASN cc_start: 0.8031 (t0) cc_final: 0.7501 (t0) REVERT: A 349 MET cc_start: 0.7177 (mtm) cc_final: 0.6854 (mtm) REVERT: A 353 SER cc_start: 0.9004 (m) cc_final: 0.8692 (p) REVERT: A 369 LYS cc_start: 0.8708 (mmtt) cc_final: 0.7943 (mmtt) REVERT: A 371 TYR cc_start: 0.8360 (m-80) cc_final: 0.7700 (m-80) REVERT: A 382 ASN cc_start: 0.8824 (m110) cc_final: 0.8573 (m110) REVERT: A 384 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 385 PHE cc_start: 0.8122 (t80) cc_final: 0.7309 (t80) REVERT: A 388 PHE cc_start: 0.8777 (m-80) cc_final: 0.8484 (m-80) REVERT: A 390 ILE cc_start: 0.8725 (mt) cc_final: 0.8502 (tp) REVERT: A 394 PHE cc_start: 0.8172 (t80) cc_final: 0.7514 (t80) REVERT: A 401 PHE cc_start: 0.7957 (p90) cc_final: 0.7573 (p90) REVERT: A 432 MET cc_start: 0.8163 (tpt) cc_final: 0.7786 (tpt) REVERT: A 438 LEU cc_start: 0.8751 (tt) cc_final: 0.8493 (tt) REVERT: A 443 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 454 VAL cc_start: 0.8972 (t) cc_final: 0.8617 (p) REVERT: A 459 LYS cc_start: 0.8516 (tppp) cc_final: 0.6413 (tppp) REVERT: A 463 MET cc_start: 0.7790 (mmp) cc_final: 0.6493 (mmp) REVERT: A 473 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8379 (mtpt) REVERT: A 476 LYS cc_start: 0.8810 (mttm) cc_final: 0.8521 (mmtt) REVERT: A 477 THR cc_start: 0.8001 (p) cc_final: 0.7768 (p) REVERT: A 478 ASP cc_start: 0.8044 (m-30) cc_final: 0.7798 (m-30) REVERT: A 486 CYS cc_start: 0.8578 (t) cc_final: 0.8348 (p) REVERT: A 487 ILE cc_start: 0.9013 (mt) cc_final: 0.8693 (pt) REVERT: A 514 GLN cc_start: 0.8095 (tt0) cc_final: 0.7588 (tm-30) REVERT: A 530 TYR cc_start: 0.8320 (m-10) cc_final: 0.7922 (m-10) REVERT: A 535 HIS cc_start: 0.7184 (m90) cc_final: 0.6967 (m-70) REVERT: A 537 LYS cc_start: 0.8598 (tttt) cc_final: 0.8312 (tttt) REVERT: A 549 ARG cc_start: 0.7586 (ttt90) cc_final: 0.6899 (ttm-80) REVERT: A 563 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8171 (mmmt) REVERT: A 564 LYS cc_start: 0.8830 (tppt) cc_final: 0.8385 (tppt) REVERT: A 681 LYS cc_start: 0.8080 (tptt) cc_final: 0.7631 (tptt) REVERT: A 682 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 685 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7756 (mtm-85) REVERT: A 687 ASP cc_start: 0.8332 (t0) cc_final: 0.7963 (t0) REVERT: A 701 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 704 GLU cc_start: 0.7396 (tt0) cc_final: 0.7154 (tt0) REVERT: A 705 GLN cc_start: 0.7942 (mm110) cc_final: 0.6749 (mm-40) REVERT: A 715 LYS cc_start: 0.8633 (mttm) cc_final: 0.8175 (ttmm) REVERT: A 724 ASP cc_start: 0.8396 (m-30) cc_final: 0.7953 (m-30) REVERT: A 727 LEU cc_start: 0.9042 (mm) cc_final: 0.8008 (mt) REVERT: A 728 HIS cc_start: 0.8827 (t70) cc_final: 0.8488 (t70) REVERT: A 731 ASN cc_start: 0.8348 (m110) cc_final: 0.8028 (m110) REVERT: B 27 TYR cc_start: 0.8612 (m-10) cc_final: 0.7931 (m-10) REVERT: B 37 GLU cc_start: 0.8054 (pp20) cc_final: 0.7606 (pp20) REVERT: B 38 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: B 122 PHE cc_start: 0.8020 (m-80) cc_final: 0.7522 (m-80) REVERT: B 124 ILE cc_start: 0.8579 (mm) cc_final: 0.8200 (pt) REVERT: B 125 LEU cc_start: 0.8783 (mt) cc_final: 0.8499 (mt) REVERT: B 144 VAL cc_start: 0.8667 (p) cc_final: 0.8213 (m) REVERT: B 147 MET cc_start: 0.8850 (mtt) cc_final: 0.8627 (mtt) REVERT: B 213 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7139 (mtp85) REVERT: B 230 GLN cc_start: 0.8383 (tp40) cc_final: 0.7756 (tp40) REVERT: B 237 LYS cc_start: 0.8914 (pttt) cc_final: 0.8339 (pttp) REVERT: B 238 ILE cc_start: 0.8704 (tp) cc_final: 0.8259 (pt) REVERT: B 250 ILE cc_start: 0.8630 (pt) cc_final: 0.8402 (tp) REVERT: B 251 LEU cc_start: 0.8657 (mm) cc_final: 0.6706 (mm) REVERT: B 254 ILE cc_start: 0.8515 (mm) cc_final: 0.7900 (tp) REVERT: B 255 TYR cc_start: 0.7455 (m-10) cc_final: 0.6792 (m-80) REVERT: B 290 ASP cc_start: 0.8452 (m-30) cc_final: 0.8242 (m-30) REVERT: B 319 LEU cc_start: 0.8664 (mt) cc_final: 0.8098 (pp) REVERT: B 323 TYR cc_start: 0.7977 (m-80) cc_final: 0.7766 (m-80) REVERT: B 324 ASN cc_start: 0.8260 (t0) cc_final: 0.7963 (t0) REVERT: B 356 ILE cc_start: 0.8225 (mt) cc_final: 0.7904 (mp) REVERT: B 455 ILE cc_start: 0.8589 (mt) cc_final: 0.7739 (mp) REVERT: B 459 LYS cc_start: 0.8746 (mmtt) cc_final: 0.7711 (mmtt) REVERT: B 463 MET cc_start: 0.6962 (mmm) cc_final: 0.6079 (mmm) REVERT: B 476 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8134 (mtpp) REVERT: B 477 THR cc_start: 0.8175 (m) cc_final: 0.7917 (p) REVERT: B 482 TRP cc_start: 0.8337 (t60) cc_final: 0.8120 (t60) REVERT: B 484 PHE cc_start: 0.8427 (t80) cc_final: 0.7864 (t80) REVERT: B 488 MET cc_start: 0.7438 (tpp) cc_final: 0.6404 (tpp) REVERT: B 491 ILE cc_start: 0.8846 (mt) cc_final: 0.8445 (mm) REVERT: B 492 LEU cc_start: 0.8695 (mt) cc_final: 0.7322 (mt) REVERT: B 494 LEU cc_start: 0.8977 (mt) cc_final: 0.8657 (mm) REVERT: B 495 ASP cc_start: 0.7443 (p0) cc_final: 0.6867 (p0) REVERT: B 496 LEU cc_start: 0.7961 (mt) cc_final: 0.7231 (mt) REVERT: B 512 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8203 (mtm-85) REVERT: B 514 GLN cc_start: 0.8734 (tt0) cc_final: 0.8291 (tm-30) REVERT: B 529 ILE cc_start: 0.8630 (mm) cc_final: 0.8400 (mm) REVERT: B 537 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7751 (mtmm) REVERT: B 563 LYS cc_start: 0.8997 (tppt) cc_final: 0.8217 (tppt) REVERT: B 577 VAL cc_start: 0.9109 (m) cc_final: 0.8848 (p) REVERT: B 666 SER cc_start: 0.8573 (p) cc_final: 0.8241 (p) REVERT: B 677 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8053 (ttm-80) REVERT: B 678 MET cc_start: 0.7955 (mmm) cc_final: 0.7670 (mmm) REVERT: B 682 GLU cc_start: 0.8225 (tp30) cc_final: 0.7921 (tp30) REVERT: B 684 GLN cc_start: 0.9125 (tp40) cc_final: 0.8774 (tp40) REVERT: B 705 GLN cc_start: 0.8390 (tt0) cc_final: 0.8123 (tt0) REVERT: B 720 LEU cc_start: 0.8977 (mp) cc_final: 0.8614 (mt) REVERT: B 724 ASP cc_start: 0.8454 (m-30) cc_final: 0.8185 (m-30) REVERT: B 727 LEU cc_start: 0.8893 (mt) cc_final: 0.8621 (mt) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.2668 time to fit residues: 130.2603 Evaluate side-chains 328 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10395 Z= 0.301 Angle : 0.661 10.591 14128 Z= 0.350 Chirality : 0.044 0.250 1716 Planarity : 0.005 0.120 1757 Dihedral : 3.868 19.296 1415 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -1.61 (0.23), residues: 1319 helix: -0.10 (0.18), residues: 834 sheet: -2.22 (0.93), residues: 34 loop : -2.81 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 74 HIS 0.004 0.001 HIS A 535 PHE 0.021 0.001 PHE B 385 TYR 0.017 0.002 TYR B 578 ARG 0.018 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 1.169 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: 0.8373 (t80) cc_final: 0.7732 (t80) REVERT: A 38 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7563 (ttm110) REVERT: A 66 LYS cc_start: 0.8822 (tppt) cc_final: 0.8106 (tppt) REVERT: A 96 LEU cc_start: 0.8923 (mt) cc_final: 0.8565 (mm) REVERT: A 103 MET cc_start: 0.8497 (mtm) cc_final: 0.7882 (mtm) REVERT: A 105 TYR cc_start: 0.8816 (m-80) cc_final: 0.8250 (m-80) REVERT: A 119 SER cc_start: 0.8676 (t) cc_final: 0.8105 (p) REVERT: A 161 PHE cc_start: 0.7835 (m-10) cc_final: 0.6822 (m-10) REVERT: A 198 ILE cc_start: 0.8620 (mt) cc_final: 0.8413 (tp) REVERT: A 211 ILE cc_start: 0.8990 (tt) cc_final: 0.8722 (tp) REVERT: A 230 GLN cc_start: 0.8834 (mt0) cc_final: 0.8178 (mt0) REVERT: A 237 LYS cc_start: 0.8969 (pttp) cc_final: 0.8678 (pttm) REVERT: A 251 LEU cc_start: 0.8333 (mt) cc_final: 0.8112 (mm) REVERT: A 252 SER cc_start: 0.8288 (p) cc_final: 0.7875 (m) REVERT: A 262 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 272 PHE cc_start: 0.8147 (t80) cc_final: 0.7755 (t80) REVERT: A 276 LEU cc_start: 0.8828 (pp) cc_final: 0.8606 (pp) REVERT: A 279 ILE cc_start: 0.9201 (mm) cc_final: 0.8454 (tt) REVERT: A 282 CYS cc_start: 0.8688 (t) cc_final: 0.8103 (p) REVERT: A 283 MET cc_start: 0.7641 (mmp) cc_final: 0.7420 (mmp) REVERT: A 286 LYS cc_start: 0.9090 (tppt) cc_final: 0.8742 (tppt) REVERT: A 289 ASN cc_start: 0.8922 (m-40) cc_final: 0.8411 (m-40) REVERT: A 306 VAL cc_start: 0.8944 (p) cc_final: 0.8560 (m) REVERT: A 309 ILE cc_start: 0.8946 (tp) cc_final: 0.8704 (pt) REVERT: A 321 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8064 (ttpp) REVERT: A 324 ASN cc_start: 0.8203 (t0) cc_final: 0.7648 (t0) REVERT: A 345 LEU cc_start: 0.8573 (mt) cc_final: 0.7741 (mp) REVERT: A 349 MET cc_start: 0.7266 (mtm) cc_final: 0.6951 (mtm) REVERT: A 353 SER cc_start: 0.9047 (m) cc_final: 0.8708 (p) REVERT: A 369 LYS cc_start: 0.8816 (mmtt) cc_final: 0.7993 (mmtt) REVERT: A 371 TYR cc_start: 0.8400 (m-80) cc_final: 0.7847 (m-80) REVERT: A 382 ASN cc_start: 0.8812 (m110) cc_final: 0.8576 (m-40) REVERT: A 384 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 385 PHE cc_start: 0.8186 (t80) cc_final: 0.7528 (t80) REVERT: A 388 PHE cc_start: 0.8978 (m-80) cc_final: 0.8517 (m-80) REVERT: A 390 ILE cc_start: 0.8831 (mt) cc_final: 0.8569 (tp) REVERT: A 392 ASN cc_start: 0.9259 (m-40) cc_final: 0.8921 (m-40) REVERT: A 394 PHE cc_start: 0.8284 (t80) cc_final: 0.7638 (t80) REVERT: A 397 PHE cc_start: 0.7800 (t80) cc_final: 0.7583 (t80) REVERT: A 409 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7563 (ttm170) REVERT: A 414 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 432 MET cc_start: 0.8332 (tpt) cc_final: 0.8006 (tpt) REVERT: A 433 VAL cc_start: 0.8814 (p) cc_final: 0.8600 (m) REVERT: A 443 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 454 VAL cc_start: 0.9141 (t) cc_final: 0.8746 (t) REVERT: A 458 LEU cc_start: 0.8859 (mt) cc_final: 0.8622 (mt) REVERT: A 459 LYS cc_start: 0.8495 (tppp) cc_final: 0.6597 (tppp) REVERT: A 463 MET cc_start: 0.7869 (mmp) cc_final: 0.6671 (mmp) REVERT: A 464 GLN cc_start: 0.8600 (mt0) cc_final: 0.8149 (mt0) REVERT: A 470 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7513 (ptt-90) REVERT: A 473 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8464 (mtpt) REVERT: A 476 LYS cc_start: 0.8795 (mttm) cc_final: 0.8514 (mmtt) REVERT: A 477 THR cc_start: 0.8138 (p) cc_final: 0.7899 (p) REVERT: A 486 CYS cc_start: 0.8845 (t) cc_final: 0.8474 (p) REVERT: A 487 ILE cc_start: 0.9045 (mt) cc_final: 0.8784 (pt) REVERT: A 496 LEU cc_start: 0.8955 (tp) cc_final: 0.8705 (tp) REVERT: A 530 TYR cc_start: 0.8401 (m-10) cc_final: 0.7943 (m-10) REVERT: A 535 HIS cc_start: 0.7425 (m90) cc_final: 0.7165 (m90) REVERT: A 537 LYS cc_start: 0.8553 (tttt) cc_final: 0.8285 (tttt) REVERT: A 540 GLU cc_start: 0.7705 (pt0) cc_final: 0.7153 (pm20) REVERT: A 549 ARG cc_start: 0.7795 (ttt90) cc_final: 0.7497 (tpp80) REVERT: A 560 ASP cc_start: 0.8406 (m-30) cc_final: 0.8059 (m-30) REVERT: A 563 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8139 (mmmt) REVERT: A 564 LYS cc_start: 0.8879 (tppt) cc_final: 0.8419 (tppt) REVERT: A 687 ASP cc_start: 0.8425 (t0) cc_final: 0.8057 (t0) REVERT: A 691 TYR cc_start: 0.7711 (m-10) cc_final: 0.7449 (m-80) REVERT: A 696 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 697 ASP cc_start: 0.8582 (m-30) cc_final: 0.7815 (p0) REVERT: A 701 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 704 GLU cc_start: 0.7468 (tt0) cc_final: 0.7191 (tt0) REVERT: A 715 LYS cc_start: 0.8574 (mttm) cc_final: 0.8170 (mttm) REVERT: A 723 HIS cc_start: 0.8419 (t70) cc_final: 0.8117 (t-90) REVERT: A 724 ASP cc_start: 0.8369 (m-30) cc_final: 0.8072 (m-30) REVERT: A 727 LEU cc_start: 0.8942 (mm) cc_final: 0.8012 (mt) REVERT: A 731 ASN cc_start: 0.8600 (m110) cc_final: 0.8019 (m-40) REVERT: B 27 TYR cc_start: 0.8818 (m-10) cc_final: 0.8108 (m-10) REVERT: B 30 LEU cc_start: 0.8427 (pt) cc_final: 0.8130 (pt) REVERT: B 37 GLU cc_start: 0.8244 (pp20) cc_final: 0.7768 (pp20) REVERT: B 122 PHE cc_start: 0.8173 (m-80) cc_final: 0.7685 (m-80) REVERT: B 124 ILE cc_start: 0.8670 (mm) cc_final: 0.8310 (pt) REVERT: B 125 LEU cc_start: 0.8827 (mt) cc_final: 0.8491 (mt) REVERT: B 137 SER cc_start: 0.7857 (t) cc_final: 0.7524 (t) REVERT: B 144 VAL cc_start: 0.8719 (p) cc_final: 0.8191 (m) REVERT: B 147 MET cc_start: 0.8990 (mtt) cc_final: 0.8743 (mtt) REVERT: B 207 GLN cc_start: 0.8838 (tt0) cc_final: 0.8529 (tm-30) REVERT: B 210 PHE cc_start: 0.6880 (p90) cc_final: 0.6629 (p90) REVERT: B 213 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7397 (mtp180) REVERT: B 236 LEU cc_start: 0.8845 (tp) cc_final: 0.8405 (tp) REVERT: B 237 LYS cc_start: 0.9102 (pttt) cc_final: 0.8532 (pttp) REVERT: B 238 ILE cc_start: 0.8717 (tp) cc_final: 0.8277 (pt) REVERT: B 241 ASN cc_start: 0.8077 (m110) cc_final: 0.7611 (m-40) REVERT: B 250 ILE cc_start: 0.8753 (pt) cc_final: 0.8511 (tp) REVERT: B 251 LEU cc_start: 0.8753 (mm) cc_final: 0.6825 (mm) REVERT: B 254 ILE cc_start: 0.8580 (mm) cc_final: 0.8048 (tp) REVERT: B 255 TYR cc_start: 0.7511 (m-10) cc_final: 0.6877 (m-80) REVERT: B 259 GLU cc_start: 0.8726 (tt0) cc_final: 0.7592 (tt0) REVERT: B 279 ILE cc_start: 0.8781 (tp) cc_final: 0.8136 (pt) REVERT: B 280 ILE cc_start: 0.8373 (mm) cc_final: 0.8150 (mm) REVERT: B 286 LYS cc_start: 0.9039 (mttt) cc_final: 0.8583 (ptpp) REVERT: B 303 GLU cc_start: 0.8924 (mp0) cc_final: 0.8684 (mp0) REVERT: B 321 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8267 (ttpp) REVERT: B 322 ASN cc_start: 0.7929 (m-40) cc_final: 0.7715 (m-40) REVERT: B 323 TYR cc_start: 0.8066 (m-80) cc_final: 0.7792 (m-80) REVERT: B 443 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6861 (tm-30) REVERT: B 450 LEU cc_start: 0.7984 (tp) cc_final: 0.7766 (tp) REVERT: B 455 ILE cc_start: 0.8785 (mt) cc_final: 0.8434 (mp) REVERT: B 459 LYS cc_start: 0.8768 (mmtt) cc_final: 0.7683 (mmtt) REVERT: B 463 MET cc_start: 0.7323 (mmm) cc_final: 0.6447 (mmm) REVERT: B 473 LYS cc_start: 0.8577 (mttp) cc_final: 0.8105 (pttp) REVERT: B 477 THR cc_start: 0.8219 (m) cc_final: 0.7873 (p) REVERT: B 482 TRP cc_start: 0.8450 (t60) cc_final: 0.8217 (t60) REVERT: B 484 PHE cc_start: 0.8519 (t80) cc_final: 0.7802 (t80) REVERT: B 488 MET cc_start: 0.7488 (tpp) cc_final: 0.6324 (tpp) REVERT: B 491 ILE cc_start: 0.8947 (mt) cc_final: 0.8550 (mm) REVERT: B 492 LEU cc_start: 0.8777 (mt) cc_final: 0.7370 (mt) REVERT: B 494 LEU cc_start: 0.9040 (mt) cc_final: 0.8638 (mm) REVERT: B 495 ASP cc_start: 0.7371 (p0) cc_final: 0.6726 (p0) REVERT: B 496 LEU cc_start: 0.7952 (mt) cc_final: 0.7176 (mt) REVERT: B 512 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8132 (mtm-85) REVERT: B 514 GLN cc_start: 0.8678 (tt0) cc_final: 0.8386 (tm-30) REVERT: B 529 ILE cc_start: 0.8663 (mm) cc_final: 0.8450 (mm) REVERT: B 537 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7909 (mtmm) REVERT: B 563 LYS cc_start: 0.8955 (tppt) cc_final: 0.8171 (tppt) REVERT: B 577 VAL cc_start: 0.9047 (m) cc_final: 0.8787 (p) REVERT: B 586 ARG cc_start: 0.8532 (ppt170) cc_final: 0.8200 (ttp80) REVERT: B 656 HIS cc_start: 0.6803 (m90) cc_final: 0.6562 (m90) REVERT: B 666 SER cc_start: 0.8710 (p) cc_final: 0.8441 (p) REVERT: B 677 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8057 (ttm-80) REVERT: B 678 MET cc_start: 0.8036 (mmm) cc_final: 0.7736 (mmm) REVERT: B 682 GLU cc_start: 0.8210 (tp30) cc_final: 0.7911 (tp30) REVERT: B 702 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7399 (tttm) REVERT: B 716 ASP cc_start: 0.8419 (p0) cc_final: 0.7472 (t0) REVERT: B 720 LEU cc_start: 0.9069 (mp) cc_final: 0.8759 (mt) REVERT: B 724 ASP cc_start: 0.8577 (m-30) cc_final: 0.8279 (m-30) REVERT: B 727 LEU cc_start: 0.9001 (mt) cc_final: 0.8332 (mt) REVERT: B 730 GLN cc_start: 0.8948 (tt0) cc_final: 0.8452 (tm-30) REVERT: B 731 ASN cc_start: 0.8432 (p0) cc_final: 0.7753 (p0) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2664 time to fit residues: 133.5493 Evaluate side-chains 352 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 567 ASN A 730 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 464 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10395 Z= 0.185 Angle : 0.593 9.134 14128 Z= 0.303 Chirality : 0.042 0.255 1716 Planarity : 0.004 0.063 1757 Dihedral : 3.890 22.902 1415 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.09 % 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: -1.06 (0.23), residues: 1319 helix: 0.37 (0.18), residues: 826 sheet: -2.18 (0.93), residues: 34 loop : -2.59 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.005 0.001 HIS A 723 PHE 0.019 0.001 PHE B 462 TYR 0.020 0.001 TYR A 27 ARG 0.010 0.001 ARG B 674 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8275 (t80) cc_final: 0.7751 (t80) REVERT: A 38 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7466 (ttm110) REVERT: A 66 LYS cc_start: 0.8766 (tppt) cc_final: 0.8075 (tppt) REVERT: A 96 LEU cc_start: 0.8877 (mt) cc_final: 0.8487 (mm) REVERT: A 103 MET cc_start: 0.8286 (mtm) cc_final: 0.7723 (ptp) REVERT: A 105 TYR cc_start: 0.8699 (m-80) cc_final: 0.8193 (m-80) REVERT: A 115 PHE cc_start: 0.8841 (m-80) cc_final: 0.8585 (m-10) REVERT: A 118 TYR cc_start: 0.8234 (m-80) cc_final: 0.7916 (m-80) REVERT: A 119 SER cc_start: 0.8764 (t) cc_final: 0.8204 (p) REVERT: A 121 PHE cc_start: 0.7834 (t80) cc_final: 0.7609 (t80) REVERT: A 161 PHE cc_start: 0.7742 (m-10) cc_final: 0.6894 (m-10) REVERT: A 194 LEU cc_start: 0.8484 (tp) cc_final: 0.8268 (mm) REVERT: A 198 ILE cc_start: 0.8572 (mt) cc_final: 0.8363 (tp) REVERT: A 211 ILE cc_start: 0.8972 (tt) cc_final: 0.8688 (tp) REVERT: A 230 GLN cc_start: 0.8797 (mt0) cc_final: 0.8297 (tp-100) REVERT: A 235 GLN cc_start: 0.8521 (mm110) cc_final: 0.8189 (mm-40) REVERT: A 237 LYS cc_start: 0.8997 (pttp) cc_final: 0.8645 (pttm) REVERT: A 251 LEU cc_start: 0.8105 (mt) cc_final: 0.7883 (mm) REVERT: A 252 SER cc_start: 0.8236 (p) cc_final: 0.7842 (m) REVERT: A 259 GLU cc_start: 0.8273 (tt0) cc_final: 0.7813 (tt0) REVERT: A 262 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 272 PHE cc_start: 0.8097 (t80) cc_final: 0.7749 (t80) REVERT: A 276 LEU cc_start: 0.8811 (pp) cc_final: 0.8483 (pp) REVERT: A 279 ILE cc_start: 0.9122 (mm) cc_final: 0.8565 (mm) REVERT: A 282 CYS cc_start: 0.8680 (t) cc_final: 0.8228 (p) REVERT: A 285 VAL cc_start: 0.8640 (m) cc_final: 0.8057 (p) REVERT: A 286 LYS cc_start: 0.9048 (tppt) cc_final: 0.8722 (tppt) REVERT: A 289 ASN cc_start: 0.8862 (m-40) cc_final: 0.8149 (m110) REVERT: A 305 ILE cc_start: 0.8632 (tp) cc_final: 0.8310 (tp) REVERT: A 309 ILE cc_start: 0.8873 (tp) cc_final: 0.8633 (pt) REVERT: A 324 ASN cc_start: 0.8205 (t0) cc_final: 0.7792 (t0) REVERT: A 345 LEU cc_start: 0.8593 (mt) cc_final: 0.7714 (mp) REVERT: A 349 MET cc_start: 0.7214 (mtm) cc_final: 0.6892 (mtm) REVERT: A 353 SER cc_start: 0.9008 (m) cc_final: 0.8665 (p) REVERT: A 369 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8018 (mmtt) REVERT: A 371 TYR cc_start: 0.8360 (m-80) cc_final: 0.7753 (m-80) REVERT: A 384 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 385 PHE cc_start: 0.8051 (t80) cc_final: 0.7261 (t80) REVERT: A 388 PHE cc_start: 0.8933 (m-80) cc_final: 0.8674 (m-80) REVERT: A 390 ILE cc_start: 0.8736 (mt) cc_final: 0.8477 (tp) REVERT: A 394 PHE cc_start: 0.8162 (t80) cc_final: 0.7539 (t80) REVERT: A 397 PHE cc_start: 0.7788 (t80) cc_final: 0.7550 (t80) REVERT: A 414 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 432 MET cc_start: 0.8298 (tpt) cc_final: 0.7863 (tpt) REVERT: A 433 VAL cc_start: 0.8797 (p) cc_final: 0.8562 (m) REVERT: A 443 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 454 VAL cc_start: 0.9113 (t) cc_final: 0.8725 (t) REVERT: A 458 LEU cc_start: 0.8825 (mt) cc_final: 0.8529 (mt) REVERT: A 459 LYS cc_start: 0.8416 (tppp) cc_final: 0.6402 (tppp) REVERT: A 461 MET cc_start: 0.8802 (mtp) cc_final: 0.8498 (mtp) REVERT: A 462 PHE cc_start: 0.8457 (m-80) cc_final: 0.8092 (m-10) REVERT: A 463 MET cc_start: 0.7751 (mmp) cc_final: 0.6649 (mmp) REVERT: A 470 ARG cc_start: 0.7867 (ptp-170) cc_final: 0.7637 (ptt-90) REVERT: A 473 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8366 (mtpt) REVERT: A 476 LYS cc_start: 0.8758 (mttm) cc_final: 0.8462 (mmtt) REVERT: A 477 THR cc_start: 0.8134 (p) cc_final: 0.7830 (p) REVERT: A 478 ASP cc_start: 0.8197 (m-30) cc_final: 0.7886 (m-30) REVERT: A 486 CYS cc_start: 0.8640 (t) cc_final: 0.8308 (p) REVERT: A 487 ILE cc_start: 0.8919 (mt) cc_final: 0.8659 (pt) REVERT: A 496 LEU cc_start: 0.8859 (tp) cc_final: 0.8601 (tp) REVERT: A 514 GLN cc_start: 0.7935 (tt0) cc_final: 0.7734 (tm-30) REVERT: A 530 TYR cc_start: 0.8279 (m-10) cc_final: 0.7915 (m-10) REVERT: A 535 HIS cc_start: 0.7326 (m90) cc_final: 0.7017 (m90) REVERT: A 537 LYS cc_start: 0.8635 (tttt) cc_final: 0.8244 (tttt) REVERT: A 538 ASN cc_start: 0.8196 (m-40) cc_final: 0.7760 (m-40) REVERT: A 549 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7080 (tpp-160) REVERT: A 560 ASP cc_start: 0.8365 (m-30) cc_final: 0.7986 (m-30) REVERT: A 563 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8116 (mmmt) REVERT: A 564 LYS cc_start: 0.8864 (tppt) cc_final: 0.8353 (tppt) REVERT: A 590 LYS cc_start: 0.8492 (pptt) cc_final: 0.8258 (tmmt) REVERT: A 678 MET cc_start: 0.8065 (mmm) cc_final: 0.7847 (mmm) REVERT: A 687 ASP cc_start: 0.8380 (t0) cc_final: 0.8008 (t0) REVERT: A 701 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 715 LYS cc_start: 0.8392 (mttm) cc_final: 0.7931 (mttm) REVERT: A 724 ASP cc_start: 0.8356 (m-30) cc_final: 0.8082 (m-30) REVERT: A 727 LEU cc_start: 0.8752 (mm) cc_final: 0.7787 (mm) REVERT: A 728 HIS cc_start: 0.8788 (t70) cc_final: 0.8453 (t70) REVERT: A 730 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: A 731 ASN cc_start: 0.8451 (m110) cc_final: 0.7987 (m110) REVERT: B 27 TYR cc_start: 0.8782 (m-10) cc_final: 0.8157 (m-10) REVERT: B 33 GLN cc_start: 0.8316 (pp30) cc_final: 0.7990 (pp30) REVERT: B 37 GLU cc_start: 0.8215 (pp20) cc_final: 0.7676 (pp20) REVERT: B 122 PHE cc_start: 0.8185 (m-80) cc_final: 0.7632 (m-80) REVERT: B 124 ILE cc_start: 0.8632 (mm) cc_final: 0.8256 (pt) REVERT: B 125 LEU cc_start: 0.8785 (mt) cc_final: 0.8425 (mt) REVERT: B 137 SER cc_start: 0.7876 (t) cc_final: 0.7554 (t) REVERT: B 144 VAL cc_start: 0.8588 (p) cc_final: 0.8105 (m) REVERT: B 147 MET cc_start: 0.8996 (mtt) cc_final: 0.8697 (mtt) REVERT: B 186 VAL cc_start: 0.9118 (p) cc_final: 0.8901 (m) REVERT: B 199 ILE cc_start: 0.8543 (tp) cc_final: 0.8339 (tp) REVERT: B 207 GLN cc_start: 0.8840 (tt0) cc_final: 0.8464 (tm-30) REVERT: B 213 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7157 (mtp180) REVERT: B 235 GLN cc_start: 0.8240 (pp30) cc_final: 0.7922 (pp30) REVERT: B 236 LEU cc_start: 0.8772 (tp) cc_final: 0.8216 (mt) REVERT: B 237 LYS cc_start: 0.8949 (pttt) cc_final: 0.8361 (pttp) REVERT: B 238 ILE cc_start: 0.8662 (tp) cc_final: 0.8233 (pt) REVERT: B 241 ASN cc_start: 0.7976 (m110) cc_final: 0.7583 (m-40) REVERT: B 250 ILE cc_start: 0.8738 (pt) cc_final: 0.8478 (tp) REVERT: B 251 LEU cc_start: 0.8757 (mm) cc_final: 0.6795 (mm) REVERT: B 254 ILE cc_start: 0.8490 (mm) cc_final: 0.7946 (tp) REVERT: B 255 TYR cc_start: 0.7425 (m-10) cc_final: 0.6872 (m-80) REVERT: B 259 GLU cc_start: 0.8659 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 260 ILE cc_start: 0.9206 (mm) cc_final: 0.8864 (mt) REVERT: B 280 ILE cc_start: 0.8354 (mm) cc_final: 0.8112 (mm) REVERT: B 286 LYS cc_start: 0.9050 (mttt) cc_final: 0.8575 (ptpp) REVERT: B 303 GLU cc_start: 0.8927 (mp0) cc_final: 0.8654 (mp0) REVERT: B 321 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8253 (ttpp) REVERT: B 323 TYR cc_start: 0.8025 (m-80) cc_final: 0.7759 (m-80) REVERT: B 324 ASN cc_start: 0.8299 (t0) cc_final: 0.8055 (t0) REVERT: B 359 VAL cc_start: 0.8933 (p) cc_final: 0.8709 (m) REVERT: B 440 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7436 (mmm160) REVERT: B 447 LYS cc_start: 0.9043 (mttt) cc_final: 0.8729 (mttm) REVERT: B 455 ILE cc_start: 0.8669 (mt) cc_final: 0.8259 (mp) REVERT: B 459 LYS cc_start: 0.8824 (mmtt) cc_final: 0.7599 (mmtt) REVERT: B 461 MET cc_start: 0.8728 (mtp) cc_final: 0.8316 (ttm) REVERT: B 463 MET cc_start: 0.7239 (mmm) cc_final: 0.6377 (mmm) REVERT: B 476 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8066 (mtpp) REVERT: B 477 THR cc_start: 0.8057 (m) cc_final: 0.7692 (p) REVERT: B 484 PHE cc_start: 0.8367 (t80) cc_final: 0.7809 (t80) REVERT: B 488 MET cc_start: 0.7426 (tpp) cc_final: 0.6276 (tpp) REVERT: B 491 ILE cc_start: 0.8895 (mt) cc_final: 0.8479 (mm) REVERT: B 492 LEU cc_start: 0.8706 (mt) cc_final: 0.7233 (mt) REVERT: B 495 ASP cc_start: 0.7435 (p0) cc_final: 0.6950 (p0) REVERT: B 496 LEU cc_start: 0.7914 (mt) cc_final: 0.7143 (mt) REVERT: B 512 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8112 (mtm-85) REVERT: B 514 GLN cc_start: 0.8655 (tt0) cc_final: 0.8370 (tm-30) REVERT: B 529 ILE cc_start: 0.8583 (mm) cc_final: 0.8306 (mm) REVERT: B 537 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7906 (mtmm) REVERT: B 563 LYS cc_start: 0.8923 (tppt) cc_final: 0.8097 (tppt) REVERT: B 577 VAL cc_start: 0.9024 (m) cc_final: 0.8733 (p) REVERT: B 578 TYR cc_start: 0.7988 (t80) cc_final: 0.7478 (t80) REVERT: B 666 SER cc_start: 0.8712 (p) cc_final: 0.8497 (p) REVERT: B 677 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7941 (ttm-80) REVERT: B 678 MET cc_start: 0.8030 (mmm) cc_final: 0.7766 (mmm) REVERT: B 682 GLU cc_start: 0.8172 (tp30) cc_final: 0.7228 (tp30) REVERT: B 685 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7371 (mtm-85) REVERT: B 719 PHE cc_start: 0.7701 (m-80) cc_final: 0.7443 (m-10) REVERT: B 720 LEU cc_start: 0.9094 (mp) cc_final: 0.8817 (mt) REVERT: B 727 LEU cc_start: 0.8895 (mt) cc_final: 0.8218 (mt) REVERT: B 730 GLN cc_start: 0.8896 (tt0) cc_final: 0.8353 (tm-30) REVERT: B 731 ASN cc_start: 0.8262 (p0) cc_final: 0.7552 (p0) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.2685 time to fit residues: 126.6877 Evaluate side-chains 352 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0570 chunk 1 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10395 Z= 0.157 Angle : 0.581 12.342 14128 Z= 0.291 Chirality : 0.042 0.387 1716 Planarity : 0.004 0.056 1757 Dihedral : 3.855 22.114 1415 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 0.56 (0.18), residues: 820 sheet: -2.02 (0.96), residues: 34 loop : -2.50 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.003 0.000 HIS A 723 PHE 0.021 0.001 PHE B 32 TYR 0.012 0.001 TYR B 105 ARG 0.006 0.001 ARG B 38 *********************** 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 360 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.051 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: 0.8221 (t80) cc_final: 0.7748 (t80) REVERT: A 38 ARG cc_start: 0.7687 (mtp-110) cc_final: 0.7412 (ttm110) REVERT: A 94 THR cc_start: 0.7435 (m) cc_final: 0.7153 (p) REVERT: A 96 LEU cc_start: 0.8790 (mt) cc_final: 0.8388 (mm) REVERT: A 103 MET cc_start: 0.8377 (mtm) cc_final: 0.8066 (mpp) REVERT: A 119 SER cc_start: 0.8708 (t) cc_final: 0.8124 (p) REVERT: A 121 PHE cc_start: 0.7770 (t80) cc_final: 0.7508 (t80) REVERT: A 161 PHE cc_start: 0.7667 (m-10) cc_final: 0.6943 (m-10) REVERT: A 194 LEU cc_start: 0.8380 (tp) cc_final: 0.8126 (mm) REVERT: A 198 ILE cc_start: 0.8540 (mt) cc_final: 0.8303 (tp) REVERT: A 210 PHE cc_start: 0.8072 (p90) cc_final: 0.7857 (p90) REVERT: A 211 ILE cc_start: 0.8937 (tt) cc_final: 0.8677 (tp) REVERT: A 230 GLN cc_start: 0.8744 (mt0) cc_final: 0.8206 (tp40) REVERT: A 237 LYS cc_start: 0.8960 (pttp) cc_final: 0.8511 (pttp) REVERT: A 251 LEU cc_start: 0.7981 (mt) cc_final: 0.7757 (mm) REVERT: A 252 SER cc_start: 0.8196 (p) cc_final: 0.7758 (m) REVERT: A 262 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 272 PHE cc_start: 0.8111 (t80) cc_final: 0.7738 (t80) REVERT: A 276 LEU cc_start: 0.8698 (pp) cc_final: 0.8412 (pp) REVERT: A 279 ILE cc_start: 0.9080 (mm) cc_final: 0.8276 (tp) REVERT: A 282 CYS cc_start: 0.8636 (t) cc_final: 0.8074 (p) REVERT: A 285 VAL cc_start: 0.8570 (m) cc_final: 0.8165 (p) REVERT: A 286 LYS cc_start: 0.9009 (tppt) cc_final: 0.8678 (tppt) REVERT: A 289 ASN cc_start: 0.8894 (m-40) cc_final: 0.8524 (m110) REVERT: A 305 ILE cc_start: 0.8609 (tp) cc_final: 0.8203 (pt) REVERT: A 309 ILE cc_start: 0.8861 (tp) cc_final: 0.8600 (pt) REVERT: A 324 ASN cc_start: 0.8145 (t0) cc_final: 0.7765 (t0) REVERT: A 345 LEU cc_start: 0.8556 (mt) cc_final: 0.7739 (mt) REVERT: A 349 MET cc_start: 0.7121 (mtm) cc_final: 0.6811 (mtm) REVERT: A 353 SER cc_start: 0.8972 (m) cc_final: 0.8634 (p) REVERT: A 369 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8527 (tppt) REVERT: A 371 TYR cc_start: 0.8349 (m-80) cc_final: 0.7780 (m-80) REVERT: A 384 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 385 PHE cc_start: 0.8003 (t80) cc_final: 0.7256 (t80) REVERT: A 388 PHE cc_start: 0.8925 (m-80) cc_final: 0.8624 (m-80) REVERT: A 394 PHE cc_start: 0.8121 (t80) cc_final: 0.7505 (t80) REVERT: A 397 PHE cc_start: 0.7740 (t80) cc_final: 0.7523 (t80) REVERT: A 414 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 432 MET cc_start: 0.8167 (tpt) cc_final: 0.7816 (tpt) REVERT: A 435 ILE cc_start: 0.8250 (mt) cc_final: 0.8023 (tp) REVERT: A 443 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 454 VAL cc_start: 0.9096 (t) cc_final: 0.8672 (t) REVERT: A 458 LEU cc_start: 0.8768 (mt) cc_final: 0.8455 (mt) REVERT: A 459 LYS cc_start: 0.8434 (tppp) cc_final: 0.6542 (tppp) REVERT: A 462 PHE cc_start: 0.8433 (m-80) cc_final: 0.8085 (m-10) REVERT: A 463 MET cc_start: 0.7731 (mmp) cc_final: 0.6803 (mmp) REVERT: A 476 LYS cc_start: 0.8657 (mttm) cc_final: 0.8376 (mmtt) REVERT: A 477 THR cc_start: 0.7996 (p) cc_final: 0.7680 (p) REVERT: A 478 ASP cc_start: 0.8093 (m-30) cc_final: 0.7701 (m-30) REVERT: A 486 CYS cc_start: 0.8570 (t) cc_final: 0.8295 (p) REVERT: A 487 ILE cc_start: 0.8884 (mt) cc_final: 0.8626 (pt) REVERT: A 496 LEU cc_start: 0.8905 (tp) cc_final: 0.8567 (tp) REVERT: A 514 GLN cc_start: 0.7926 (tt0) cc_final: 0.7710 (tm-30) REVERT: A 530 TYR cc_start: 0.8200 (m-10) cc_final: 0.7814 (m-80) REVERT: A 537 LYS cc_start: 0.8633 (tttt) cc_final: 0.8272 (tttt) REVERT: A 538 ASN cc_start: 0.8187 (m-40) cc_final: 0.7773 (m-40) REVERT: A 549 ARG cc_start: 0.7605 (ttt90) cc_final: 0.7060 (tpp-160) REVERT: A 560 ASP cc_start: 0.8314 (m-30) cc_final: 0.7950 (m-30) REVERT: A 563 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8100 (mmmt) REVERT: A 564 LYS cc_start: 0.8847 (tppt) cc_final: 0.8412 (tppt) REVERT: A 580 LYS cc_start: 0.7753 (tttt) cc_final: 0.7424 (tttp) REVERT: A 590 LYS cc_start: 0.8495 (pptt) cc_final: 0.8206 (tmmt) REVERT: A 678 MET cc_start: 0.8046 (mmm) cc_final: 0.7705 (mmm) REVERT: A 687 ASP cc_start: 0.8375 (t0) cc_final: 0.8018 (t0) REVERT: A 701 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 705 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7483 (tp-100) REVERT: A 723 HIS cc_start: 0.8130 (t70) cc_final: 0.7821 (t-90) REVERT: A 724 ASP cc_start: 0.8406 (m-30) cc_final: 0.7833 (m-30) REVERT: A 727 LEU cc_start: 0.9022 (mm) cc_final: 0.7319 (mt) REVERT: A 728 HIS cc_start: 0.8745 (t70) cc_final: 0.8379 (t70) REVERT: A 731 ASN cc_start: 0.8598 (m110) cc_final: 0.7805 (m110) REVERT: B 27 TYR cc_start: 0.8724 (m-10) cc_final: 0.8104 (m-10) REVERT: B 30 LEU cc_start: 0.8352 (pt) cc_final: 0.8111 (pp) REVERT: B 33 GLN cc_start: 0.8296 (pp30) cc_final: 0.7963 (pp30) REVERT: B 37 GLU cc_start: 0.8130 (pp20) cc_final: 0.7669 (pp20) REVERT: B 105 TYR cc_start: 0.7280 (m-80) cc_final: 0.6769 (m-80) REVERT: B 122 PHE cc_start: 0.8204 (m-80) cc_final: 0.7651 (m-80) REVERT: B 124 ILE cc_start: 0.8621 (mm) cc_final: 0.8267 (pt) REVERT: B 125 LEU cc_start: 0.8739 (mt) cc_final: 0.8467 (mt) REVERT: B 137 SER cc_start: 0.7876 (t) cc_final: 0.7547 (t) REVERT: B 144 VAL cc_start: 0.8610 (p) cc_final: 0.8063 (m) REVERT: B 147 MET cc_start: 0.9031 (mtt) cc_final: 0.8746 (mtt) REVERT: B 186 VAL cc_start: 0.9109 (p) cc_final: 0.8795 (m) REVERT: B 199 ILE cc_start: 0.8444 (tp) cc_final: 0.8224 (tp) REVERT: B 207 GLN cc_start: 0.8795 (tt0) cc_final: 0.8424 (tm-30) REVERT: B 230 GLN cc_start: 0.8421 (pp30) cc_final: 0.7889 (pp30) REVERT: B 236 LEU cc_start: 0.8792 (tp) cc_final: 0.8418 (tp) REVERT: B 237 LYS cc_start: 0.8899 (pttt) cc_final: 0.8387 (pttp) REVERT: B 238 ILE cc_start: 0.8641 (tp) cc_final: 0.8304 (pt) REVERT: B 250 ILE cc_start: 0.8708 (pt) cc_final: 0.8339 (mm) REVERT: B 251 LEU cc_start: 0.8672 (mm) cc_final: 0.6747 (mm) REVERT: B 255 TYR cc_start: 0.7428 (m-10) cc_final: 0.6972 (m-80) REVERT: B 259 GLU cc_start: 0.8663 (tt0) cc_final: 0.8291 (tm-30) REVERT: B 260 ILE cc_start: 0.9179 (mm) cc_final: 0.8792 (mt) REVERT: B 279 ILE cc_start: 0.8531 (tp) cc_final: 0.8147 (pt) REVERT: B 280 ILE cc_start: 0.8312 (mm) cc_final: 0.8111 (mm) REVERT: B 286 LYS cc_start: 0.9091 (mttt) cc_final: 0.8642 (ptpp) REVERT: B 303 GLU cc_start: 0.8907 (mp0) cc_final: 0.8637 (mp0) REVERT: B 321 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8343 (ttpp) REVERT: B 322 ASN cc_start: 0.7901 (m-40) cc_final: 0.7682 (t0) REVERT: B 323 TYR cc_start: 0.7998 (m-80) cc_final: 0.6865 (m-80) REVERT: B 359 VAL cc_start: 0.8897 (p) cc_final: 0.8659 (m) REVERT: B 447 LYS cc_start: 0.9024 (mttt) cc_final: 0.8802 (mttp) REVERT: B 455 ILE cc_start: 0.8551 (mt) cc_final: 0.8203 (mp) REVERT: B 459 LYS cc_start: 0.8714 (mmtt) cc_final: 0.7462 (mmtt) REVERT: B 461 MET cc_start: 0.8663 (mtp) cc_final: 0.8043 (ttm) REVERT: B 463 MET cc_start: 0.7145 (mmm) cc_final: 0.6272 (mmm) REVERT: B 473 LYS cc_start: 0.8492 (mttp) cc_final: 0.7589 (pttt) REVERT: B 476 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8022 (mtpp) REVERT: B 477 THR cc_start: 0.8264 (m) cc_final: 0.7998 (p) REVERT: B 484 PHE cc_start: 0.8280 (t80) cc_final: 0.7757 (t80) REVERT: B 488 MET cc_start: 0.7335 (tpp) cc_final: 0.5973 (tpp) REVERT: B 491 ILE cc_start: 0.8891 (mt) cc_final: 0.8613 (mm) REVERT: B 492 LEU cc_start: 0.8648 (mt) cc_final: 0.7256 (mt) REVERT: B 495 ASP cc_start: 0.7410 (p0) cc_final: 0.6882 (p0) REVERT: B 496 LEU cc_start: 0.7880 (mt) cc_final: 0.7076 (mt) REVERT: B 512 ARG cc_start: 0.8581 (mtm180) cc_final: 0.8082 (mtm-85) REVERT: B 514 GLN cc_start: 0.8639 (tt0) cc_final: 0.8339 (tm-30) REVERT: B 529 ILE cc_start: 0.8625 (mm) cc_final: 0.8383 (mm) REVERT: B 535 HIS cc_start: 0.7496 (m90) cc_final: 0.7284 (m90) REVERT: B 537 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7919 (mtmm) REVERT: B 558 ASN cc_start: 0.7868 (p0) cc_final: 0.7667 (p0) REVERT: B 563 LYS cc_start: 0.8923 (tppt) cc_final: 0.7802 (tppt) REVERT: B 567 ASN cc_start: 0.8192 (m-40) cc_final: 0.7356 (m110) REVERT: B 577 VAL cc_start: 0.9079 (m) cc_final: 0.8763 (p) REVERT: B 590 LYS cc_start: 0.8509 (pttp) cc_final: 0.8041 (ptmm) REVERT: B 594 LYS cc_start: 0.8523 (pttm) cc_final: 0.8167 (pttm) REVERT: B 666 SER cc_start: 0.8624 (p) cc_final: 0.8340 (p) REVERT: B 674 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8086 (ttm110) REVERT: B 677 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7984 (ttm-80) REVERT: B 678 MET cc_start: 0.8034 (mmm) cc_final: 0.7782 (mmm) REVERT: B 682 GLU cc_start: 0.8144 (tp30) cc_final: 0.7692 (tp30) REVERT: B 719 PHE cc_start: 0.7787 (m-80) cc_final: 0.7534 (m-10) REVERT: B 720 LEU cc_start: 0.9076 (mp) cc_final: 0.8802 (mt) REVERT: B 727 LEU cc_start: 0.8896 (mt) cc_final: 0.7609 (mt) REVERT: B 730 GLN cc_start: 0.8889 (tt0) cc_final: 0.8407 (pp30) REVERT: B 731 ASN cc_start: 0.8219 (p0) cc_final: 0.7795 (p0) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.2680 time to fit residues: 126.6816 Evaluate side-chains 342 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 375 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10395 Z= 0.179 Angle : 0.596 9.117 14128 Z= 0.301 Chirality : 0.042 0.286 1716 Planarity : 0.004 0.046 1757 Dihedral : 3.913 23.125 1415 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -0.81 (0.23), residues: 1319 helix: 0.55 (0.18), residues: 834 sheet: -1.98 (0.97), residues: 34 loop : -2.51 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 518 HIS 0.007 0.001 HIS A 723 PHE 0.019 0.001 PHE B 385 TYR 0.020 0.001 TYR A 105 ARG 0.007 0.001 ARG B 38 *********************** 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 352 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.139 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: 0.8272 (t80) cc_final: 0.7788 (t80) REVERT: A 38 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7245 (ttm110) REVERT: A 94 THR cc_start: 0.7509 (m) cc_final: 0.7236 (p) REVERT: A 96 LEU cc_start: 0.8782 (mt) cc_final: 0.8410 (mm) REVERT: A 103 MET cc_start: 0.8441 (mtm) cc_final: 0.8119 (mpp) REVERT: A 119 SER cc_start: 0.8675 (t) cc_final: 0.8164 (p) REVERT: A 121 PHE cc_start: 0.7782 (t80) cc_final: 0.7464 (t80) REVERT: A 161 PHE cc_start: 0.7743 (m-10) cc_final: 0.6974 (m-10) REVERT: A 194 LEU cc_start: 0.8346 (tp) cc_final: 0.8101 (mm) REVERT: A 198 ILE cc_start: 0.8525 (mt) cc_final: 0.8301 (tp) REVERT: A 211 ILE cc_start: 0.8949 (tt) cc_final: 0.8700 (tp) REVERT: A 230 GLN cc_start: 0.8786 (mt0) cc_final: 0.8258 (tp40) REVERT: A 234 SER cc_start: 0.9157 (m) cc_final: 0.8804 (p) REVERT: A 235 GLN cc_start: 0.8448 (mm110) cc_final: 0.8027 (mm-40) REVERT: A 237 LYS cc_start: 0.8971 (pttp) cc_final: 0.8565 (pttp) REVERT: A 251 LEU cc_start: 0.8083 (mt) cc_final: 0.7857 (mm) REVERT: A 252 SER cc_start: 0.8258 (p) cc_final: 0.7891 (m) REVERT: A 259 GLU cc_start: 0.8389 (tt0) cc_final: 0.8146 (tt0) REVERT: A 262 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 272 PHE cc_start: 0.8173 (t80) cc_final: 0.7734 (t80) REVERT: A 276 LEU cc_start: 0.8689 (pp) cc_final: 0.8365 (pp) REVERT: A 279 ILE cc_start: 0.9068 (mm) cc_final: 0.8217 (tp) REVERT: A 282 CYS cc_start: 0.8600 (t) cc_final: 0.8038 (p) REVERT: A 283 MET cc_start: 0.7436 (mmp) cc_final: 0.7174 (mmp) REVERT: A 285 VAL cc_start: 0.8521 (m) cc_final: 0.8109 (p) REVERT: A 286 LYS cc_start: 0.9034 (tppt) cc_final: 0.8791 (tppt) REVERT: A 289 ASN cc_start: 0.8905 (m-40) cc_final: 0.8381 (m110) REVERT: A 305 ILE cc_start: 0.8673 (tp) cc_final: 0.8297 (pt) REVERT: A 309 ILE cc_start: 0.8894 (tp) cc_final: 0.8631 (pt) REVERT: A 324 ASN cc_start: 0.8204 (t0) cc_final: 0.7782 (t0) REVERT: A 345 LEU cc_start: 0.8447 (mt) cc_final: 0.7567 (mt) REVERT: A 349 MET cc_start: 0.6964 (mtm) cc_final: 0.6641 (mtm) REVERT: A 353 SER cc_start: 0.9019 (m) cc_final: 0.8668 (p) REVERT: A 369 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8530 (tppt) REVERT: A 371 TYR cc_start: 0.8324 (m-80) cc_final: 0.7827 (m-80) REVERT: A 384 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8029 (mm-30) REVERT: A 385 PHE cc_start: 0.8050 (t80) cc_final: 0.7313 (t80) REVERT: A 388 PHE cc_start: 0.8897 (m-80) cc_final: 0.8498 (m-80) REVERT: A 394 PHE cc_start: 0.8167 (t80) cc_final: 0.7499 (t80) REVERT: A 397 PHE cc_start: 0.7789 (t80) cc_final: 0.7555 (t80) REVERT: A 414 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 432 MET cc_start: 0.8290 (tpt) cc_final: 0.7814 (tpt) REVERT: A 433 VAL cc_start: 0.8849 (p) cc_final: 0.8644 (m) REVERT: A 443 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 454 VAL cc_start: 0.9103 (t) cc_final: 0.8743 (t) REVERT: A 458 LEU cc_start: 0.8799 (mt) cc_final: 0.8512 (mt) REVERT: A 459 LYS cc_start: 0.8399 (tppp) cc_final: 0.6460 (tppp) REVERT: A 462 PHE cc_start: 0.8475 (m-80) cc_final: 0.8151 (m-10) REVERT: A 463 MET cc_start: 0.7781 (mmp) cc_final: 0.6675 (mmp) REVERT: A 470 ARG cc_start: 0.7935 (ptt90) cc_final: 0.7632 (ptt-90) REVERT: A 473 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8420 (mtpt) REVERT: A 476 LYS cc_start: 0.8659 (mttm) cc_final: 0.8371 (mmtt) REVERT: A 477 THR cc_start: 0.8027 (p) cc_final: 0.7732 (p) REVERT: A 478 ASP cc_start: 0.8018 (m-30) cc_final: 0.7596 (m-30) REVERT: A 486 CYS cc_start: 0.8633 (t) cc_final: 0.8349 (p) REVERT: A 487 ILE cc_start: 0.8905 (mt) cc_final: 0.8645 (pt) REVERT: A 496 LEU cc_start: 0.8868 (tp) cc_final: 0.8602 (tp) REVERT: A 514 GLN cc_start: 0.8016 (tt0) cc_final: 0.7751 (tm-30) REVERT: A 530 TYR cc_start: 0.8222 (m-10) cc_final: 0.7990 (m-80) REVERT: A 535 HIS cc_start: 0.7150 (m90) cc_final: 0.6489 (m90) REVERT: A 537 LYS cc_start: 0.8594 (tttt) cc_final: 0.7882 (tttt) REVERT: A 538 ASN cc_start: 0.8192 (m-40) cc_final: 0.7825 (m-40) REVERT: A 549 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7157 (tpp-160) REVERT: A 560 ASP cc_start: 0.8326 (m-30) cc_final: 0.7957 (m-30) REVERT: A 563 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8092 (mmmt) REVERT: A 564 LYS cc_start: 0.8868 (tppt) cc_final: 0.8384 (tppt) REVERT: A 580 LYS cc_start: 0.7846 (tttt) cc_final: 0.7343 (tttp) REVERT: A 590 LYS cc_start: 0.8514 (pptt) cc_final: 0.8241 (tmmt) REVERT: A 678 MET cc_start: 0.8063 (mmm) cc_final: 0.7694 (mmm) REVERT: A 687 ASP cc_start: 0.8395 (t0) cc_final: 0.8044 (t0) REVERT: A 694 LEU cc_start: 0.8899 (mt) cc_final: 0.8689 (mt) REVERT: A 701 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 705 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7593 (tp-100) REVERT: A 724 ASP cc_start: 0.8410 (m-30) cc_final: 0.7813 (m-30) REVERT: A 728 HIS cc_start: 0.8785 (t70) cc_final: 0.8519 (t70) REVERT: A 731 ASN cc_start: 0.8451 (m110) cc_final: 0.8101 (m110) REVERT: B 27 TYR cc_start: 0.8763 (m-10) cc_final: 0.8155 (m-10) REVERT: B 30 LEU cc_start: 0.8385 (pt) cc_final: 0.8152 (pp) REVERT: B 33 GLN cc_start: 0.8387 (pp30) cc_final: 0.8057 (pp30) REVERT: B 39 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7719 (mtt180) REVERT: B 105 TYR cc_start: 0.7316 (m-80) cc_final: 0.6854 (m-80) REVERT: B 122 PHE cc_start: 0.8271 (m-80) cc_final: 0.7694 (m-80) REVERT: B 124 ILE cc_start: 0.8655 (mm) cc_final: 0.8271 (pt) REVERT: B 125 LEU cc_start: 0.8760 (mt) cc_final: 0.8486 (mt) REVERT: B 137 SER cc_start: 0.7895 (t) cc_final: 0.7580 (t) REVERT: B 144 VAL cc_start: 0.8586 (p) cc_final: 0.8015 (m) REVERT: B 147 MET cc_start: 0.9041 (mtt) cc_final: 0.8671 (mtt) REVERT: B 186 VAL cc_start: 0.9059 (p) cc_final: 0.8762 (m) REVERT: B 196 VAL cc_start: 0.8955 (t) cc_final: 0.8649 (t) REVERT: B 199 ILE cc_start: 0.8516 (tp) cc_final: 0.8268 (tp) REVERT: B 200 GLN cc_start: 0.8560 (mt0) cc_final: 0.8338 (mt0) REVERT: B 207 GLN cc_start: 0.8842 (tt0) cc_final: 0.8484 (tm-30) REVERT: B 213 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7039 (mtp180) REVERT: B 236 LEU cc_start: 0.8825 (tp) cc_final: 0.8381 (tp) REVERT: B 237 LYS cc_start: 0.8954 (pttt) cc_final: 0.8197 (pttp) REVERT: B 238 ILE cc_start: 0.8700 (tp) cc_final: 0.8378 (pt) REVERT: B 250 ILE cc_start: 0.8736 (pt) cc_final: 0.8373 (mm) REVERT: B 251 LEU cc_start: 0.8650 (mm) cc_final: 0.6810 (mm) REVERT: B 255 TYR cc_start: 0.7483 (m-10) cc_final: 0.7028 (m-80) REVERT: B 259 GLU cc_start: 0.8676 (tt0) cc_final: 0.7767 (tt0) REVERT: B 279 ILE cc_start: 0.8576 (tp) cc_final: 0.8187 (pt) REVERT: B 280 ILE cc_start: 0.8345 (mm) cc_final: 0.8136 (mm) REVERT: B 283 MET cc_start: 0.7969 (ptp) cc_final: 0.7646 (ptp) REVERT: B 303 GLU cc_start: 0.8912 (mp0) cc_final: 0.8661 (mp0) REVERT: B 321 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8200 (ttpp) REVERT: B 323 TYR cc_start: 0.8070 (m-80) cc_final: 0.7730 (m-80) REVERT: B 324 ASN cc_start: 0.8284 (t0) cc_final: 0.8068 (t0) REVERT: B 447 LYS cc_start: 0.9059 (mttt) cc_final: 0.8583 (mttm) REVERT: B 455 ILE cc_start: 0.8587 (mt) cc_final: 0.8259 (mp) REVERT: B 459 LYS cc_start: 0.8734 (mmtt) cc_final: 0.7554 (mmtt) REVERT: B 461 MET cc_start: 0.8730 (mtp) cc_final: 0.8170 (ttm) REVERT: B 463 MET cc_start: 0.7188 (mmm) cc_final: 0.6306 (mmm) REVERT: B 467 ASP cc_start: 0.8568 (m-30) cc_final: 0.8063 (m-30) REVERT: B 473 LYS cc_start: 0.8455 (mttp) cc_final: 0.7606 (pttt) REVERT: B 477 THR cc_start: 0.8252 (m) cc_final: 0.8025 (p) REVERT: B 484 PHE cc_start: 0.8299 (t80) cc_final: 0.7743 (t80) REVERT: B 488 MET cc_start: 0.7384 (tpp) cc_final: 0.6183 (tpp) REVERT: B 491 ILE cc_start: 0.8897 (mt) cc_final: 0.8639 (mm) REVERT: B 492 LEU cc_start: 0.8668 (mt) cc_final: 0.7282 (mt) REVERT: B 495 ASP cc_start: 0.7391 (p0) cc_final: 0.6836 (p0) REVERT: B 496 LEU cc_start: 0.7891 (mt) cc_final: 0.7076 (mt) REVERT: B 512 ARG cc_start: 0.8592 (mtm180) cc_final: 0.8074 (mtm-85) REVERT: B 514 GLN cc_start: 0.8637 (tt0) cc_final: 0.8359 (tm-30) REVERT: B 529 ILE cc_start: 0.8646 (mm) cc_final: 0.8312 (mp) REVERT: B 535 HIS cc_start: 0.7570 (m90) cc_final: 0.7313 (m90) REVERT: B 563 LYS cc_start: 0.8949 (tppt) cc_final: 0.8111 (tppt) REVERT: B 577 VAL cc_start: 0.9068 (m) cc_final: 0.8764 (p) REVERT: B 666 SER cc_start: 0.8633 (p) cc_final: 0.8387 (p) REVERT: B 674 ARG cc_start: 0.8868 (ttm110) cc_final: 0.8093 (ttm110) REVERT: B 677 ARG cc_start: 0.8315 (ttt180) cc_final: 0.7840 (ttm-80) REVERT: B 678 MET cc_start: 0.8027 (mmm) cc_final: 0.7794 (mmm) REVERT: B 682 GLU cc_start: 0.7908 (tp30) cc_final: 0.7605 (tp30) REVERT: B 691 TYR cc_start: 0.7700 (m-80) cc_final: 0.7082 (m-80) REVERT: B 703 MET cc_start: 0.8154 (mtm) cc_final: 0.7752 (mtm) REVERT: B 719 PHE cc_start: 0.7876 (m-80) cc_final: 0.7653 (m-10) REVERT: B 720 LEU cc_start: 0.9118 (mp) cc_final: 0.8828 (mt) REVERT: B 727 LEU cc_start: 0.8887 (mt) cc_final: 0.7495 (mt) REVERT: B 730 GLN cc_start: 0.8904 (tt0) cc_final: 0.8471 (pp30) REVERT: B 731 ASN cc_start: 0.8215 (p0) cc_final: 0.7250 (p0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2716 time to fit residues: 125.0248 Evaluate side-chains 322 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 322 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10395 Z= 0.177 Angle : 0.595 9.498 14128 Z= 0.301 Chirality : 0.042 0.299 1716 Planarity : 0.004 0.046 1757 Dihedral : 3.907 23.652 1415 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.24 % 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: -0.66 (0.23), residues: 1319 helix: 0.62 (0.18), residues: 842 sheet: -1.73 (1.00), residues: 34 loop : -2.41 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 74 HIS 0.003 0.000 HIS A 723 PHE 0.016 0.001 PHE B 562 TYR 0.021 0.001 TYR B 578 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.105 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: 0.8275 (t80) cc_final: 0.7830 (t80) REVERT: A 38 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7410 (ttm110) REVERT: A 66 LYS cc_start: 0.8882 (tptt) cc_final: 0.8674 (tptt) REVERT: A 96 LEU cc_start: 0.8787 (mt) cc_final: 0.8406 (mm) REVERT: A 103 MET cc_start: 0.8529 (mtm) cc_final: 0.8234 (mpp) REVERT: A 119 SER cc_start: 0.8628 (t) cc_final: 0.8141 (p) REVERT: A 121 PHE cc_start: 0.7692 (t80) cc_final: 0.7383 (t80) REVERT: A 147 MET cc_start: 0.8522 (mtp) cc_final: 0.8308 (mtp) REVERT: A 161 PHE cc_start: 0.7617 (m-10) cc_final: 0.6283 (m-10) REVERT: A 194 LEU cc_start: 0.8329 (tp) cc_final: 0.8084 (mm) REVERT: A 198 ILE cc_start: 0.8498 (mt) cc_final: 0.8279 (tp) REVERT: A 211 ILE cc_start: 0.8939 (tt) cc_final: 0.8712 (tp) REVERT: A 230 GLN cc_start: 0.8761 (mt0) cc_final: 0.8254 (tp40) REVERT: A 234 SER cc_start: 0.9199 (m) cc_final: 0.8790 (p) REVERT: A 235 GLN cc_start: 0.8434 (mm110) cc_final: 0.7973 (mm-40) REVERT: A 237 LYS cc_start: 0.8980 (pttp) cc_final: 0.8498 (pttp) REVERT: A 251 LEU cc_start: 0.8086 (mt) cc_final: 0.7831 (mm) REVERT: A 252 SER cc_start: 0.8285 (p) cc_final: 0.7859 (m) REVERT: A 262 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 272 PHE cc_start: 0.8090 (t80) cc_final: 0.7762 (t80) REVERT: A 276 LEU cc_start: 0.8702 (pp) cc_final: 0.8423 (pp) REVERT: A 279 ILE cc_start: 0.9051 (mm) cc_final: 0.8125 (tp) REVERT: A 281 VAL cc_start: 0.8800 (m) cc_final: 0.8561 (p) REVERT: A 282 CYS cc_start: 0.8597 (t) cc_final: 0.7994 (p) REVERT: A 283 MET cc_start: 0.7414 (mmp) cc_final: 0.7084 (mmp) REVERT: A 285 VAL cc_start: 0.8529 (m) cc_final: 0.8017 (p) REVERT: A 286 LYS cc_start: 0.9038 (tppt) cc_final: 0.8789 (tppt) REVERT: A 289 ASN cc_start: 0.8908 (m-40) cc_final: 0.8188 (m110) REVERT: A 305 ILE cc_start: 0.8655 (tp) cc_final: 0.8433 (tp) REVERT: A 309 ILE cc_start: 0.8907 (tp) cc_final: 0.8669 (pt) REVERT: A 324 ASN cc_start: 0.8238 (t0) cc_final: 0.7824 (t0) REVERT: A 345 LEU cc_start: 0.8454 (mt) cc_final: 0.7568 (mt) REVERT: A 349 MET cc_start: 0.6990 (mtm) cc_final: 0.6677 (mtm) REVERT: A 353 SER cc_start: 0.8991 (m) cc_final: 0.8654 (p) REVERT: A 369 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8529 (tppt) REVERT: A 371 TYR cc_start: 0.8370 (m-80) cc_final: 0.7856 (m-80) REVERT: A 384 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 385 PHE cc_start: 0.8024 (t80) cc_final: 0.7290 (t80) REVERT: A 388 PHE cc_start: 0.8874 (m-80) cc_final: 0.8531 (m-80) REVERT: A 394 PHE cc_start: 0.8164 (t80) cc_final: 0.7497 (t80) REVERT: A 397 PHE cc_start: 0.7789 (t80) cc_final: 0.7589 (t80) REVERT: A 414 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 432 MET cc_start: 0.8272 (tpt) cc_final: 0.7720 (tpt) REVERT: A 433 VAL cc_start: 0.8867 (p) cc_final: 0.8638 (m) REVERT: A 443 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 447 LYS cc_start: 0.9274 (mtpt) cc_final: 0.8904 (mtmt) REVERT: A 454 VAL cc_start: 0.9125 (t) cc_final: 0.8762 (t) REVERT: A 458 LEU cc_start: 0.8822 (mt) cc_final: 0.8592 (mt) REVERT: A 459 LYS cc_start: 0.8331 (tppp) cc_final: 0.6408 (tppp) REVERT: A 462 PHE cc_start: 0.8413 (m-80) cc_final: 0.8070 (m-80) REVERT: A 463 MET cc_start: 0.7750 (mmp) cc_final: 0.6638 (mmp) REVERT: A 470 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7623 (ptt-90) REVERT: A 473 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8396 (mtpt) REVERT: A 476 LYS cc_start: 0.8663 (mttm) cc_final: 0.8315 (mmtp) REVERT: A 477 THR cc_start: 0.8062 (p) cc_final: 0.7787 (p) REVERT: A 478 ASP cc_start: 0.8050 (m-30) cc_final: 0.7669 (m-30) REVERT: A 486 CYS cc_start: 0.8630 (t) cc_final: 0.8354 (p) REVERT: A 487 ILE cc_start: 0.8899 (mt) cc_final: 0.8641 (pt) REVERT: A 496 LEU cc_start: 0.8955 (tp) cc_final: 0.8627 (tp) REVERT: A 514 GLN cc_start: 0.8013 (tt0) cc_final: 0.7768 (tm-30) REVERT: A 530 TYR cc_start: 0.8176 (m-10) cc_final: 0.7843 (m-80) REVERT: A 531 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8192 (mmmt) REVERT: A 535 HIS cc_start: 0.7073 (m90) cc_final: 0.6445 (m90) REVERT: A 537 LYS cc_start: 0.8599 (tttt) cc_final: 0.8189 (tttt) REVERT: A 538 ASN cc_start: 0.8188 (m-40) cc_final: 0.7760 (m-40) REVERT: A 549 ARG cc_start: 0.7645 (ttt90) cc_final: 0.7194 (tpp-160) REVERT: A 560 ASP cc_start: 0.8341 (m-30) cc_final: 0.7995 (m-30) REVERT: A 563 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8059 (mmmt) REVERT: A 564 LYS cc_start: 0.8865 (tppt) cc_final: 0.8444 (tppt) REVERT: A 580 LYS cc_start: 0.7872 (tttt) cc_final: 0.7157 (tttp) REVERT: A 590 LYS cc_start: 0.8545 (pptt) cc_final: 0.8248 (tmmt) REVERT: A 678 MET cc_start: 0.8084 (mmm) cc_final: 0.7697 (mmm) REVERT: A 687 ASP cc_start: 0.8415 (t0) cc_final: 0.8047 (t0) REVERT: A 701 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 705 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7623 (tp-100) REVERT: A 724 ASP cc_start: 0.8401 (m-30) cc_final: 0.7828 (m-30) REVERT: A 727 LEU cc_start: 0.8711 (mm) cc_final: 0.8127 (mt) REVERT: A 728 HIS cc_start: 0.8785 (t70) cc_final: 0.8535 (t70) REVERT: A 731 ASN cc_start: 0.8501 (m110) cc_final: 0.8132 (m110) REVERT: B 27 TYR cc_start: 0.8790 (m-10) cc_final: 0.8164 (m-10) REVERT: B 30 LEU cc_start: 0.8385 (pt) cc_final: 0.8153 (pp) REVERT: B 33 GLN cc_start: 0.8396 (pp30) cc_final: 0.8056 (pp30) REVERT: B 37 GLU cc_start: 0.8114 (pp20) cc_final: 0.7687 (pp20) REVERT: B 38 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7915 (tpp80) REVERT: B 105 TYR cc_start: 0.7269 (m-80) cc_final: 0.6791 (m-80) REVERT: B 122 PHE cc_start: 0.8347 (m-80) cc_final: 0.7783 (m-80) REVERT: B 124 ILE cc_start: 0.8707 (mm) cc_final: 0.8328 (pt) REVERT: B 125 LEU cc_start: 0.8790 (mt) cc_final: 0.8507 (mt) REVERT: B 137 SER cc_start: 0.8042 (t) cc_final: 0.7691 (t) REVERT: B 144 VAL cc_start: 0.8569 (p) cc_final: 0.8051 (m) REVERT: B 147 MET cc_start: 0.9032 (mtt) cc_final: 0.8672 (mtt) REVERT: B 186 VAL cc_start: 0.9014 (p) cc_final: 0.8719 (m) REVERT: B 199 ILE cc_start: 0.8476 (tp) cc_final: 0.8210 (tp) REVERT: B 207 GLN cc_start: 0.8862 (tt0) cc_final: 0.8462 (tm-30) REVERT: B 213 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7278 (mtp180) REVERT: B 230 GLN cc_start: 0.8505 (pp30) cc_final: 0.7895 (pp30) REVERT: B 236 LEU cc_start: 0.8826 (tp) cc_final: 0.8430 (tp) REVERT: B 237 LYS cc_start: 0.8949 (pttt) cc_final: 0.8397 (pttp) REVERT: B 238 ILE cc_start: 0.8720 (tp) cc_final: 0.8374 (pt) REVERT: B 250 ILE cc_start: 0.8713 (pt) cc_final: 0.8371 (mm) REVERT: B 251 LEU cc_start: 0.8662 (mm) cc_final: 0.6813 (mm) REVERT: B 255 TYR cc_start: 0.7523 (m-10) cc_final: 0.7032 (m-80) REVERT: B 259 GLU cc_start: 0.8673 (tt0) cc_final: 0.8271 (tm-30) REVERT: B 260 ILE cc_start: 0.9182 (mm) cc_final: 0.8795 (mt) REVERT: B 279 ILE cc_start: 0.8575 (tp) cc_final: 0.8191 (pt) REVERT: B 280 ILE cc_start: 0.8366 (mm) cc_final: 0.8145 (mm) REVERT: B 286 LYS cc_start: 0.9048 (mttt) cc_final: 0.8716 (ptpp) REVERT: B 303 GLU cc_start: 0.8893 (mp0) cc_final: 0.8621 (mp0) REVERT: B 318 ASN cc_start: 0.8596 (t0) cc_final: 0.8018 (t0) REVERT: B 321 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8300 (ttpp) REVERT: B 322 ASN cc_start: 0.8069 (m110) cc_final: 0.7644 (t0) REVERT: B 323 TYR cc_start: 0.8073 (m-80) cc_final: 0.6889 (m-80) REVERT: B 324 ASN cc_start: 0.8246 (t0) cc_final: 0.8021 (t0) REVERT: B 447 LYS cc_start: 0.9065 (mttt) cc_final: 0.8863 (mttt) REVERT: B 455 ILE cc_start: 0.8551 (mt) cc_final: 0.8273 (mp) REVERT: B 459 LYS cc_start: 0.8729 (mmtt) cc_final: 0.7504 (mmtt) REVERT: B 461 MET cc_start: 0.8719 (mtp) cc_final: 0.8169 (ttm) REVERT: B 463 MET cc_start: 0.7152 (mmm) cc_final: 0.6283 (mmm) REVERT: B 467 ASP cc_start: 0.8562 (m-30) cc_final: 0.8063 (m-30) REVERT: B 473 LYS cc_start: 0.8467 (mttp) cc_final: 0.7606 (pttt) REVERT: B 477 THR cc_start: 0.8253 (m) cc_final: 0.8005 (p) REVERT: B 484 PHE cc_start: 0.8287 (t80) cc_final: 0.7736 (t80) REVERT: B 488 MET cc_start: 0.7381 (tpp) cc_final: 0.6017 (tpp) REVERT: B 491 ILE cc_start: 0.8864 (mt) cc_final: 0.8630 (mm) REVERT: B 492 LEU cc_start: 0.8639 (mt) cc_final: 0.7177 (mt) REVERT: B 496 LEU cc_start: 0.7890 (mt) cc_final: 0.7579 (mm) REVERT: B 512 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8162 (mtm-85) REVERT: B 514 GLN cc_start: 0.8613 (tt0) cc_final: 0.8369 (tm-30) REVERT: B 529 ILE cc_start: 0.8656 (mm) cc_final: 0.8388 (mm) REVERT: B 535 HIS cc_start: 0.7510 (m90) cc_final: 0.7241 (m90) REVERT: B 537 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7892 (mtmm) REVERT: B 563 LYS cc_start: 0.8996 (tppt) cc_final: 0.7759 (tppt) REVERT: B 567 ASN cc_start: 0.8169 (m-40) cc_final: 0.7408 (m110) REVERT: B 577 VAL cc_start: 0.9071 (m) cc_final: 0.8774 (p) REVERT: B 656 HIS cc_start: 0.6918 (m90) cc_final: 0.6670 (m90) REVERT: B 666 SER cc_start: 0.8639 (p) cc_final: 0.8393 (p) REVERT: B 674 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8134 (ttm110) REVERT: B 677 ARG cc_start: 0.8293 (ttt180) cc_final: 0.7839 (ttm-80) REVERT: B 678 MET cc_start: 0.8020 (mmm) cc_final: 0.7784 (mmm) REVERT: B 682 GLU cc_start: 0.7925 (tp30) cc_final: 0.7651 (tp30) REVERT: B 691 TYR cc_start: 0.7694 (m-80) cc_final: 0.7076 (m-80) REVERT: B 720 LEU cc_start: 0.9133 (mp) cc_final: 0.8832 (mt) REVERT: B 727 LEU cc_start: 0.8900 (mt) cc_final: 0.8429 (mt) REVERT: B 730 GLN cc_start: 0.8913 (tt0) cc_final: 0.8308 (pp30) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2584 time to fit residues: 119.4162 Evaluate side-chains 327 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.0270 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4906 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= 0.162 Angle : 0.591 9.697 14128 Z= 0.299 Chirality : 0.042 0.311 1716 Planarity : 0.004 0.054 1757 Dihedral : 3.920 23.799 1415 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.59 (0.23), residues: 1319 helix: 0.65 (0.18), residues: 837 sheet: -1.71 (0.99), residues: 34 loop : -2.31 (0.28), residues: 448 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 0.017 0.001 PHE B 562 TYR 0.016 0.001 TYR B 578 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8248 (t80) cc_final: 0.7822 (t80) REVERT: A 59 LYS cc_start: 0.8374 (tptt) cc_final: 0.8124 (mmmt) REVERT: A 96 LEU cc_start: 0.8737 (mt) cc_final: 0.8360 (mm) REVERT: A 105 TYR cc_start: 0.8216 (m-80) cc_final: 0.7924 (m-80) REVERT: A 119 SER cc_start: 0.8516 (t) cc_final: 0.8068 (p) REVERT: A 121 PHE cc_start: 0.7640 (t80) cc_final: 0.7367 (t80) REVERT: A 161 PHE cc_start: 0.7563 (m-10) cc_final: 0.6599 (m-10) REVERT: A 194 LEU cc_start: 0.8311 (tp) cc_final: 0.8074 (mm) REVERT: A 198 ILE cc_start: 0.8497 (mt) cc_final: 0.8261 (tp) REVERT: A 200 GLN cc_start: 0.8643 (mt0) cc_final: 0.7686 (tt0) REVERT: A 211 ILE cc_start: 0.8924 (tt) cc_final: 0.8684 (tp) REVERT: A 230 GLN cc_start: 0.8741 (mt0) cc_final: 0.8122 (tp40) REVERT: A 234 SER cc_start: 0.9168 (m) cc_final: 0.8831 (p) REVERT: A 235 GLN cc_start: 0.8508 (mm110) cc_final: 0.8053 (mm-40) REVERT: A 237 LYS cc_start: 0.8938 (pttp) cc_final: 0.8516 (pttp) REVERT: A 245 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8340 (mmmt) REVERT: A 251 LEU cc_start: 0.8035 (mt) cc_final: 0.7791 (mm) REVERT: A 252 SER cc_start: 0.8268 (p) cc_final: 0.7845 (m) REVERT: A 262 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 263 ASN cc_start: 0.8993 (t0) cc_final: 0.8484 (t0) REVERT: A 272 PHE cc_start: 0.8066 (t80) cc_final: 0.7818 (t80) REVERT: A 276 LEU cc_start: 0.8690 (pp) cc_final: 0.8383 (pp) REVERT: A 279 ILE cc_start: 0.9038 (mm) cc_final: 0.8129 (tp) REVERT: A 282 CYS cc_start: 0.8580 (t) cc_final: 0.7995 (p) REVERT: A 283 MET cc_start: 0.7371 (mmp) cc_final: 0.7058 (mmp) REVERT: A 285 VAL cc_start: 0.8529 (m) cc_final: 0.8175 (p) REVERT: A 286 LYS cc_start: 0.9020 (tppt) cc_final: 0.8725 (tppt) REVERT: A 289 ASN cc_start: 0.8900 (m-40) cc_final: 0.8510 (m110) REVERT: A 305 ILE cc_start: 0.8613 (tp) cc_final: 0.8381 (tp) REVERT: A 309 ILE cc_start: 0.8894 (tp) cc_final: 0.8648 (pt) REVERT: A 324 ASN cc_start: 0.8231 (t0) cc_final: 0.7847 (t0) REVERT: A 345 LEU cc_start: 0.8459 (mt) cc_final: 0.7533 (mt) REVERT: A 349 MET cc_start: 0.7034 (mtm) cc_final: 0.6707 (mtm) REVERT: A 353 SER cc_start: 0.8975 (m) cc_final: 0.8665 (p) REVERT: A 369 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8538 (tppt) REVERT: A 371 TYR cc_start: 0.8346 (m-80) cc_final: 0.7827 (m-80) REVERT: A 384 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 388 PHE cc_start: 0.8849 (m-80) cc_final: 0.8406 (m-80) REVERT: A 392 ASN cc_start: 0.9168 (m-40) cc_final: 0.8916 (m-40) REVERT: A 394 PHE cc_start: 0.8134 (t80) cc_final: 0.7580 (t80) REVERT: A 414 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 432 MET cc_start: 0.8268 (tpt) cc_final: 0.7740 (tpt) REVERT: A 433 VAL cc_start: 0.8854 (p) cc_final: 0.8639 (m) REVERT: A 443 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 447 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8837 (mtmt) REVERT: A 454 VAL cc_start: 0.9104 (t) cc_final: 0.8804 (t) REVERT: A 458 LEU cc_start: 0.8851 (mt) cc_final: 0.8421 (mt) REVERT: A 459 LYS cc_start: 0.8213 (tppp) cc_final: 0.6377 (tppp) REVERT: A 461 MET cc_start: 0.8799 (ptm) cc_final: 0.8587 (ptm) REVERT: A 463 MET cc_start: 0.7717 (mmp) cc_final: 0.6740 (mmp) REVERT: A 470 ARG cc_start: 0.7898 (ptt90) cc_final: 0.7515 (ptt180) REVERT: A 473 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8380 (mtpt) REVERT: A 476 LYS cc_start: 0.8674 (mttm) cc_final: 0.8361 (mmtt) REVERT: A 477 THR cc_start: 0.8042 (p) cc_final: 0.7802 (p) REVERT: A 478 ASP cc_start: 0.8070 (m-30) cc_final: 0.7705 (m-30) REVERT: A 486 CYS cc_start: 0.8597 (t) cc_final: 0.8363 (p) REVERT: A 487 ILE cc_start: 0.8856 (mt) cc_final: 0.8550 (pt) REVERT: A 496 LEU cc_start: 0.8861 (tp) cc_final: 0.8367 (tp) REVERT: A 503 LEU cc_start: 0.9244 (mt) cc_final: 0.8995 (mm) REVERT: A 514 GLN cc_start: 0.8004 (tt0) cc_final: 0.7726 (tm-30) REVERT: A 530 TYR cc_start: 0.8154 (m-10) cc_final: 0.7828 (m-80) REVERT: A 535 HIS cc_start: 0.6962 (m90) cc_final: 0.6474 (m90) REVERT: A 537 LYS cc_start: 0.8578 (tttt) cc_final: 0.8219 (tttt) REVERT: A 538 ASN cc_start: 0.8151 (m-40) cc_final: 0.7814 (m-40) REVERT: A 549 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7012 (tpp-160) REVERT: A 560 ASP cc_start: 0.8262 (m-30) cc_final: 0.7845 (m-30) REVERT: A 563 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8119 (mmmt) REVERT: A 564 LYS cc_start: 0.8881 (tppt) cc_final: 0.8450 (tppt) REVERT: A 580 LYS cc_start: 0.7632 (tttt) cc_final: 0.7363 (tttp) REVERT: A 590 LYS cc_start: 0.8553 (pptt) cc_final: 0.8242 (tmmt) REVERT: A 678 MET cc_start: 0.8058 (mmm) cc_final: 0.7693 (mmm) REVERT: A 687 ASP cc_start: 0.8403 (t0) cc_final: 0.8048 (t0) REVERT: A 689 ASN cc_start: 0.7881 (m-40) cc_final: 0.7492 (m-40) REVERT: A 701 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 705 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7628 (tp-100) REVERT: A 724 ASP cc_start: 0.8363 (m-30) cc_final: 0.7768 (m-30) REVERT: A 727 LEU cc_start: 0.8697 (mm) cc_final: 0.8086 (mt) REVERT: A 728 HIS cc_start: 0.8793 (t70) cc_final: 0.8514 (t70) REVERT: A 731 ASN cc_start: 0.8466 (m110) cc_final: 0.8104 (m110) REVERT: B 27 TYR cc_start: 0.8800 (m-10) cc_final: 0.8134 (m-10) REVERT: B 33 GLN cc_start: 0.8388 (pp30) cc_final: 0.8064 (pp30) REVERT: B 37 GLU cc_start: 0.8100 (pp20) cc_final: 0.7799 (pp20) REVERT: B 38 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7891 (tpp80) REVERT: B 105 TYR cc_start: 0.7262 (m-80) cc_final: 0.6865 (m-80) REVERT: B 122 PHE cc_start: 0.8311 (m-80) cc_final: 0.7737 (m-80) REVERT: B 124 ILE cc_start: 0.8680 (mm) cc_final: 0.8315 (pt) REVERT: B 125 LEU cc_start: 0.8756 (mt) cc_final: 0.8478 (mt) REVERT: B 137 SER cc_start: 0.8109 (t) cc_final: 0.7788 (t) REVERT: B 144 VAL cc_start: 0.8543 (p) cc_final: 0.8031 (m) REVERT: B 147 MET cc_start: 0.9021 (mtt) cc_final: 0.8762 (mtt) REVERT: B 186 VAL cc_start: 0.9009 (p) cc_final: 0.8723 (m) REVERT: B 199 ILE cc_start: 0.8388 (tp) cc_final: 0.7760 (pt) REVERT: B 207 GLN cc_start: 0.8837 (tt0) cc_final: 0.8428 (tm-30) REVERT: B 213 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7221 (mtp180) REVERT: B 236 LEU cc_start: 0.8798 (tp) cc_final: 0.8316 (tp) REVERT: B 237 LYS cc_start: 0.8948 (pttt) cc_final: 0.8353 (pttp) REVERT: B 238 ILE cc_start: 0.8702 (tp) cc_final: 0.8372 (pt) REVERT: B 240 LEU cc_start: 0.9042 (mm) cc_final: 0.8749 (mm) REVERT: B 250 ILE cc_start: 0.8715 (pt) cc_final: 0.8361 (mm) REVERT: B 251 LEU cc_start: 0.8662 (mm) cc_final: 0.6848 (mm) REVERT: B 255 TYR cc_start: 0.7509 (m-10) cc_final: 0.7020 (m-80) REVERT: B 259 GLU cc_start: 0.8678 (tt0) cc_final: 0.7835 (tt0) REVERT: B 279 ILE cc_start: 0.8542 (tp) cc_final: 0.8153 (pt) REVERT: B 286 LYS cc_start: 0.9031 (mttt) cc_final: 0.8651 (ptpp) REVERT: B 293 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8263 (mmtm) REVERT: B 303 GLU cc_start: 0.8891 (mp0) cc_final: 0.8607 (mp0) REVERT: B 321 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8319 (ttpp) REVERT: B 323 TYR cc_start: 0.8052 (m-80) cc_final: 0.7726 (m-80) REVERT: B 324 ASN cc_start: 0.8210 (t0) cc_final: 0.7964 (t0) REVERT: B 359 VAL cc_start: 0.8952 (p) cc_final: 0.8726 (m) REVERT: B 432 MET cc_start: 0.8397 (ppp) cc_final: 0.8159 (ppp) REVERT: B 455 ILE cc_start: 0.8472 (mt) cc_final: 0.8104 (mp) REVERT: B 459 LYS cc_start: 0.8719 (mmtt) cc_final: 0.7510 (mmtt) REVERT: B 461 MET cc_start: 0.8698 (mtp) cc_final: 0.7961 (ttm) REVERT: B 463 MET cc_start: 0.7148 (mmm) cc_final: 0.6248 (mmm) REVERT: B 467 ASP cc_start: 0.8570 (m-30) cc_final: 0.8042 (m-30) REVERT: B 477 THR cc_start: 0.8203 (m) cc_final: 0.7864 (p) REVERT: B 484 PHE cc_start: 0.8276 (t80) cc_final: 0.7727 (t80) REVERT: B 488 MET cc_start: 0.7323 (tpp) cc_final: 0.5960 (tpp) REVERT: B 491 ILE cc_start: 0.8841 (mt) cc_final: 0.8587 (mm) REVERT: B 492 LEU cc_start: 0.8611 (mt) cc_final: 0.7131 (mt) REVERT: B 496 LEU cc_start: 0.7867 (mt) cc_final: 0.7616 (mt) REVERT: B 514 GLN cc_start: 0.8626 (tt0) cc_final: 0.8344 (tp40) REVERT: B 529 ILE cc_start: 0.8640 (mm) cc_final: 0.8411 (mm) REVERT: B 535 HIS cc_start: 0.7570 (m90) cc_final: 0.7315 (m90) REVERT: B 537 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7874 (mtmm) REVERT: B 563 LYS cc_start: 0.8936 (tppt) cc_final: 0.8086 (tppt) REVERT: B 577 VAL cc_start: 0.9068 (m) cc_final: 0.8760 (p) REVERT: B 580 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8423 (tptt) REVERT: B 656 HIS cc_start: 0.7012 (m90) cc_final: 0.6766 (m90) REVERT: B 666 SER cc_start: 0.8595 (p) cc_final: 0.8362 (p) REVERT: B 674 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8119 (ttm110) REVERT: B 677 ARG cc_start: 0.8322 (ttt180) cc_final: 0.7876 (ttm-80) REVERT: B 678 MET cc_start: 0.8023 (mmm) cc_final: 0.7781 (mmm) REVERT: B 682 GLU cc_start: 0.7956 (tp30) cc_final: 0.7642 (tp30) REVERT: B 691 TYR cc_start: 0.7668 (m-80) cc_final: 0.7020 (m-80) REVERT: B 720 LEU cc_start: 0.9160 (mp) cc_final: 0.8820 (mt) REVERT: B 727 LEU cc_start: 0.8867 (mt) cc_final: 0.8300 (mt) REVERT: B 730 GLN cc_start: 0.8895 (tt0) cc_final: 0.8349 (pp30) REVERT: B 731 ASN cc_start: 0.8132 (p0) cc_final: 0.7723 (p0) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2682 time to fit residues: 124.6754 Evaluate side-chains 324 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5085 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= 0.206 Angle : 0.621 10.938 14128 Z= 0.316 Chirality : 0.043 0.321 1716 Planarity : 0.004 0.056 1757 Dihedral : 4.015 23.090 1415 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1319 helix: 0.74 (0.18), residues: 833 sheet: -1.90 (0.95), residues: 34 loop : -2.26 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 74 HIS 0.002 0.000 HIS A 723 PHE 0.024 0.001 PHE B 203 TYR 0.023 0.002 TYR B 578 ARG 0.010 0.001 ARG B 586 *********************** 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 367 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.092 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: 0.8304 (t80) cc_final: 0.7828 (t80) REVERT: A 59 LYS cc_start: 0.8393 (tptt) cc_final: 0.8167 (mmmt) REVERT: A 96 LEU cc_start: 0.8747 (mt) cc_final: 0.8395 (mm) REVERT: A 103 MET cc_start: 0.8543 (mtm) cc_final: 0.7681 (mtm) REVERT: A 105 TYR cc_start: 0.8360 (m-80) cc_final: 0.8077 (m-80) REVERT: A 119 SER cc_start: 0.8529 (t) cc_final: 0.8128 (p) REVERT: A 121 PHE cc_start: 0.7670 (t80) cc_final: 0.7336 (t80) REVERT: A 161 PHE cc_start: 0.7641 (m-10) cc_final: 0.6759 (m-10) REVERT: A 194 LEU cc_start: 0.8350 (tp) cc_final: 0.8132 (mm) REVERT: A 198 ILE cc_start: 0.8510 (mt) cc_final: 0.8304 (tp) REVERT: A 211 ILE cc_start: 0.8961 (tt) cc_final: 0.8753 (tp) REVERT: A 213 ARG cc_start: 0.7247 (mtt180) cc_final: 0.6947 (mtt-85) REVERT: A 230 GLN cc_start: 0.8772 (mt0) cc_final: 0.8128 (tp40) REVERT: A 234 SER cc_start: 0.9168 (m) cc_final: 0.8843 (p) REVERT: A 235 GLN cc_start: 0.8540 (mm110) cc_final: 0.8088 (mm-40) REVERT: A 237 LYS cc_start: 0.8956 (pttp) cc_final: 0.8545 (pttp) REVERT: A 240 LEU cc_start: 0.8582 (mm) cc_final: 0.8346 (mp) REVERT: A 251 LEU cc_start: 0.8157 (mt) cc_final: 0.7899 (mm) REVERT: A 252 SER cc_start: 0.8334 (p) cc_final: 0.7945 (m) REVERT: A 262 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 263 ASN cc_start: 0.9016 (t0) cc_final: 0.8542 (t0) REVERT: A 272 PHE cc_start: 0.8126 (t80) cc_final: 0.7836 (t80) REVERT: A 276 LEU cc_start: 0.8698 (pp) cc_final: 0.8381 (pp) REVERT: A 279 ILE cc_start: 0.9029 (mm) cc_final: 0.8383 (tp) REVERT: A 281 VAL cc_start: 0.8835 (m) cc_final: 0.8620 (p) REVERT: A 283 MET cc_start: 0.7398 (mmp) cc_final: 0.7088 (mmp) REVERT: A 285 VAL cc_start: 0.8610 (m) cc_final: 0.8243 (p) REVERT: A 286 LYS cc_start: 0.9035 (tppt) cc_final: 0.8744 (tppt) REVERT: A 289 ASN cc_start: 0.8915 (m-40) cc_final: 0.8537 (m110) REVERT: A 305 ILE cc_start: 0.8669 (tp) cc_final: 0.8438 (tp) REVERT: A 309 ILE cc_start: 0.8924 (tp) cc_final: 0.8681 (pt) REVERT: A 324 ASN cc_start: 0.8222 (t0) cc_final: 0.7850 (t0) REVERT: A 345 LEU cc_start: 0.8428 (mt) cc_final: 0.7474 (mt) REVERT: A 349 MET cc_start: 0.7059 (mtm) cc_final: 0.6732 (mtm) REVERT: A 353 SER cc_start: 0.8983 (m) cc_final: 0.8675 (p) REVERT: A 369 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8595 (tppt) REVERT: A 371 TYR cc_start: 0.8355 (m-80) cc_final: 0.7863 (m-80) REVERT: A 383 GLN cc_start: 0.8800 (mm110) cc_final: 0.8312 (mm-40) REVERT: A 385 PHE cc_start: 0.7981 (t80) cc_final: 0.7229 (t80) REVERT: A 388 PHE cc_start: 0.8907 (m-80) cc_final: 0.8641 (m-80) REVERT: A 392 ASN cc_start: 0.9147 (m-40) cc_final: 0.8776 (m-40) REVERT: A 394 PHE cc_start: 0.8174 (t80) cc_final: 0.7633 (t80) REVERT: A 397 PHE cc_start: 0.7697 (t80) cc_final: 0.7248 (t80) REVERT: A 414 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 432 MET cc_start: 0.8358 (tpt) cc_final: 0.7838 (tpt) REVERT: A 433 VAL cc_start: 0.8885 (p) cc_final: 0.8681 (m) REVERT: A 443 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 447 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8875 (mtmt) REVERT: A 454 VAL cc_start: 0.9072 (t) cc_final: 0.8724 (t) REVERT: A 459 LYS cc_start: 0.8271 (tppp) cc_final: 0.6557 (tppp) REVERT: A 463 MET cc_start: 0.7873 (mmp) cc_final: 0.6789 (mmp) REVERT: A 470 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7610 (ptt-90) REVERT: A 473 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8375 (mtpt) REVERT: A 476 LYS cc_start: 0.8727 (mttm) cc_final: 0.8353 (mmtp) REVERT: A 477 THR cc_start: 0.8115 (p) cc_final: 0.7830 (p) REVERT: A 478 ASP cc_start: 0.8074 (m-30) cc_final: 0.7683 (m-30) REVERT: A 486 CYS cc_start: 0.8661 (t) cc_final: 0.8365 (p) REVERT: A 487 ILE cc_start: 0.8895 (mt) cc_final: 0.8568 (pt) REVERT: A 496 LEU cc_start: 0.8917 (tp) cc_final: 0.8464 (tp) REVERT: A 503 LEU cc_start: 0.9266 (mt) cc_final: 0.9007 (mm) REVERT: A 514 GLN cc_start: 0.8001 (tt0) cc_final: 0.7777 (tm-30) REVERT: A 530 TYR cc_start: 0.8136 (m-10) cc_final: 0.7844 (m-10) REVERT: A 535 HIS cc_start: 0.7209 (m90) cc_final: 0.6983 (m90) REVERT: A 536 TYR cc_start: 0.8221 (m-80) cc_final: 0.7979 (m-80) REVERT: A 537 LYS cc_start: 0.8608 (tttt) cc_final: 0.8246 (tttt) REVERT: A 538 ASN cc_start: 0.8166 (m-40) cc_final: 0.7826 (m-40) REVERT: A 549 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7096 (tpp-160) REVERT: A 560 ASP cc_start: 0.8285 (m-30) cc_final: 0.7851 (m-30) REVERT: A 563 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8083 (mmmt) REVERT: A 564 LYS cc_start: 0.8890 (tppt) cc_final: 0.8462 (tppt) REVERT: A 567 ASN cc_start: 0.8272 (m-40) cc_final: 0.8064 (m-40) REVERT: A 590 LYS cc_start: 0.8569 (pptt) cc_final: 0.8262 (tmmt) REVERT: A 678 MET cc_start: 0.8113 (mmm) cc_final: 0.7736 (mmm) REVERT: A 687 ASP cc_start: 0.8429 (t0) cc_final: 0.8065 (t0) REVERT: A 705 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7643 (tp-100) REVERT: A 724 ASP cc_start: 0.8430 (m-30) cc_final: 0.7880 (m-30) REVERT: A 727 LEU cc_start: 0.8762 (mm) cc_final: 0.8295 (mm) REVERT: A 728 HIS cc_start: 0.8801 (t70) cc_final: 0.8410 (t-90) REVERT: A 731 ASN cc_start: 0.8489 (m110) cc_final: 0.8131 (m110) REVERT: B 27 TYR cc_start: 0.8828 (m-10) cc_final: 0.8205 (m-10) REVERT: B 30 LEU cc_start: 0.8410 (pt) cc_final: 0.8195 (pp) REVERT: B 32 PHE cc_start: 0.8281 (t80) cc_final: 0.8006 (t80) REVERT: B 33 GLN cc_start: 0.8411 (pp30) cc_final: 0.8088 (pp30) REVERT: B 37 GLU cc_start: 0.8294 (pp20) cc_final: 0.7965 (pp20) REVERT: B 38 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7937 (tpp80) REVERT: B 105 TYR cc_start: 0.7325 (m-80) cc_final: 0.6955 (m-80) REVERT: B 122 PHE cc_start: 0.8337 (m-80) cc_final: 0.7739 (m-80) REVERT: B 124 ILE cc_start: 0.8751 (mm) cc_final: 0.8363 (pt) REVERT: B 125 LEU cc_start: 0.8814 (mt) cc_final: 0.8555 (mt) REVERT: B 137 SER cc_start: 0.8023 (t) cc_final: 0.7705 (t) REVERT: B 144 VAL cc_start: 0.8589 (p) cc_final: 0.8061 (m) REVERT: B 147 MET cc_start: 0.9046 (mtt) cc_final: 0.8708 (mtt) REVERT: B 186 VAL cc_start: 0.8997 (p) cc_final: 0.8687 (m) REVERT: B 207 GLN cc_start: 0.8865 (tt0) cc_final: 0.8422 (tm-30) REVERT: B 213 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7239 (mtp180) REVERT: B 236 LEU cc_start: 0.8838 (tp) cc_final: 0.8531 (tp) REVERT: B 237 LYS cc_start: 0.9006 (pttt) cc_final: 0.8406 (pttp) REVERT: B 238 ILE cc_start: 0.8754 (tp) cc_final: 0.8407 (pt) REVERT: B 250 ILE cc_start: 0.8746 (pt) cc_final: 0.8405 (mm) REVERT: B 251 LEU cc_start: 0.8677 (mm) cc_final: 0.6883 (mm) REVERT: B 255 TYR cc_start: 0.7549 (m-10) cc_final: 0.7052 (m-80) REVERT: B 259 GLU cc_start: 0.8704 (tt0) cc_final: 0.8313 (tm-30) REVERT: B 260 ILE cc_start: 0.9193 (mm) cc_final: 0.8830 (mt) REVERT: B 261 PHE cc_start: 0.8222 (m-10) cc_final: 0.7956 (m-10) REVERT: B 279 ILE cc_start: 0.8587 (tp) cc_final: 0.8257 (pt) REVERT: B 303 GLU cc_start: 0.8910 (mp0) cc_final: 0.8621 (mp0) REVERT: B 318 ASN cc_start: 0.8495 (t0) cc_final: 0.8038 (t0) REVERT: B 321 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8345 (ttpp) REVERT: B 322 ASN cc_start: 0.8019 (m110) cc_final: 0.7376 (t0) REVERT: B 323 TYR cc_start: 0.8101 (m-80) cc_final: 0.6901 (m-80) REVERT: B 432 MET cc_start: 0.8430 (ppp) cc_final: 0.8198 (ppp) REVERT: B 447 LYS cc_start: 0.9106 (mttt) cc_final: 0.8777 (mptt) REVERT: B 455 ILE cc_start: 0.8555 (mt) cc_final: 0.8245 (mp) REVERT: B 459 LYS cc_start: 0.8732 (mmtt) cc_final: 0.7549 (mmtt) REVERT: B 463 MET cc_start: 0.7265 (mmm) cc_final: 0.6293 (mmm) REVERT: B 473 LYS cc_start: 0.8511 (mttp) cc_final: 0.7602 (mtmm) REVERT: B 476 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7914 (mmmm) REVERT: B 484 PHE cc_start: 0.8309 (t80) cc_final: 0.7704 (t80) REVERT: B 488 MET cc_start: 0.7402 (tpp) cc_final: 0.6020 (tpp) REVERT: B 491 ILE cc_start: 0.8876 (mt) cc_final: 0.8619 (mm) REVERT: B 492 LEU cc_start: 0.8641 (mt) cc_final: 0.7269 (mt) REVERT: B 495 ASP cc_start: 0.7427 (p0) cc_final: 0.6885 (p0) REVERT: B 496 LEU cc_start: 0.7894 (mt) cc_final: 0.7054 (mt) REVERT: B 512 ARG cc_start: 0.8655 (mtm180) cc_final: 0.8015 (mtm-85) REVERT: B 514 GLN cc_start: 0.8600 (tt0) cc_final: 0.8384 (tm-30) REVERT: B 537 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7955 (mtmm) REVERT: B 563 LYS cc_start: 0.8985 (tppt) cc_final: 0.7771 (tppt) REVERT: B 567 ASN cc_start: 0.8179 (m-40) cc_final: 0.7461 (m110) REVERT: B 577 VAL cc_start: 0.9076 (m) cc_final: 0.8775 (p) REVERT: B 656 HIS cc_start: 0.7092 (m90) cc_final: 0.6785 (m90) REVERT: B 674 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8146 (ttm110) REVERT: B 677 ARG cc_start: 0.8293 (ttt180) cc_final: 0.7896 (ttm-80) REVERT: B 678 MET cc_start: 0.8032 (mmm) cc_final: 0.7804 (mmm) REVERT: B 682 GLU cc_start: 0.7954 (tp30) cc_final: 0.7672 (tp30) REVERT: B 691 TYR cc_start: 0.7696 (m-80) cc_final: 0.6984 (m-80) REVERT: B 716 ASP cc_start: 0.8336 (p0) cc_final: 0.8089 (p0) REVERT: B 720 LEU cc_start: 0.9182 (mp) cc_final: 0.8848 (mp) REVERT: B 727 LEU cc_start: 0.8878 (mt) cc_final: 0.8454 (mt) REVERT: B 730 GLN cc_start: 0.8934 (tt0) cc_final: 0.8341 (pp30) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2768 time to fit residues: 134.2244 Evaluate side-chains 330 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10395 Z= 0.279 Angle : 0.681 10.402 14128 Z= 0.357 Chirality : 0.045 0.346 1716 Planarity : 0.004 0.055 1757 Dihedral : 4.303 22.833 1415 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % 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: -0.68 (0.23), residues: 1319 helix: 0.53 (0.18), residues: 836 sheet: -2.21 (0.92), residues: 34 loop : -2.18 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 472 HIS 0.003 0.001 HIS A 135 PHE 0.033 0.002 PHE B 335 TYR 0.022 0.002 TYR B 578 ARG 0.006 0.001 ARG B 38 ********************** 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 360 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.106 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: 0.8410 (t80) cc_final: 0.7991 (t80) REVERT: A 29 GLU cc_start: 0.8173 (tp30) cc_final: 0.7811 (tp30) REVERT: A 38 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7522 (ttm110) REVERT: A 59 LYS cc_start: 0.8450 (tptt) cc_final: 0.8167 (mmmt) REVERT: A 66 LYS cc_start: 0.9005 (tptt) cc_final: 0.8440 (tptp) REVERT: A 96 LEU cc_start: 0.8781 (mt) cc_final: 0.8443 (mm) REVERT: A 99 THR cc_start: 0.8974 (t) cc_final: 0.8164 (t) REVERT: A 103 MET cc_start: 0.8647 (mtm) cc_final: 0.8367 (mpp) REVERT: A 105 TYR cc_start: 0.8615 (m-80) cc_final: 0.8412 (m-80) REVERT: A 119 SER cc_start: 0.8530 (t) cc_final: 0.8123 (p) REVERT: A 121 PHE cc_start: 0.7791 (t80) cc_final: 0.7312 (t80) REVERT: A 161 PHE cc_start: 0.7790 (m-10) cc_final: 0.6938 (m-10) REVERT: A 198 ILE cc_start: 0.8587 (mt) cc_final: 0.8367 (tp) REVERT: A 211 ILE cc_start: 0.9071 (tt) cc_final: 0.8823 (tp) REVERT: A 217 ASP cc_start: 0.8767 (t0) cc_final: 0.8561 (t0) REVERT: A 230 GLN cc_start: 0.8719 (mt0) cc_final: 0.8071 (tp40) REVERT: A 234 SER cc_start: 0.9209 (m) cc_final: 0.8741 (p) REVERT: A 235 GLN cc_start: 0.8553 (mm110) cc_final: 0.8097 (mm-40) REVERT: A 237 LYS cc_start: 0.8978 (pttp) cc_final: 0.8592 (pttm) REVERT: A 251 LEU cc_start: 0.8302 (mt) cc_final: 0.8003 (mm) REVERT: A 252 SER cc_start: 0.8488 (p) cc_final: 0.8136 (m) REVERT: A 262 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 272 PHE cc_start: 0.8243 (t80) cc_final: 0.7875 (t80) REVERT: A 276 LEU cc_start: 0.8751 (pp) cc_final: 0.8402 (pp) REVERT: A 279 ILE cc_start: 0.9038 (mm) cc_final: 0.8387 (tp) REVERT: A 281 VAL cc_start: 0.8876 (m) cc_final: 0.8667 (p) REVERT: A 282 CYS cc_start: 0.8556 (t) cc_final: 0.8065 (p) REVERT: A 283 MET cc_start: 0.7455 (mmp) cc_final: 0.7139 (mmp) REVERT: A 285 VAL cc_start: 0.8710 (m) cc_final: 0.8308 (p) REVERT: A 286 LYS cc_start: 0.9084 (tppt) cc_final: 0.8755 (tppt) REVERT: A 289 ASN cc_start: 0.8923 (m-40) cc_final: 0.8532 (m110) REVERT: A 305 ILE cc_start: 0.8720 (tp) cc_final: 0.8520 (tp) REVERT: A 309 ILE cc_start: 0.8967 (tp) cc_final: 0.8714 (pt) REVERT: A 324 ASN cc_start: 0.8280 (t0) cc_final: 0.7879 (t0) REVERT: A 345 LEU cc_start: 0.8477 (mt) cc_final: 0.7544 (mp) REVERT: A 349 MET cc_start: 0.7022 (mtm) cc_final: 0.6583 (mtm) REVERT: A 353 SER cc_start: 0.8986 (m) cc_final: 0.8661 (p) REVERT: A 369 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8657 (tppt) REVERT: A 371 TYR cc_start: 0.8343 (m-80) cc_final: 0.7855 (m-80) REVERT: A 383 GLN cc_start: 0.8850 (mm110) cc_final: 0.8383 (mm-40) REVERT: A 385 PHE cc_start: 0.8137 (t80) cc_final: 0.7344 (t80) REVERT: A 388 PHE cc_start: 0.8949 (m-80) cc_final: 0.8709 (m-80) REVERT: A 394 PHE cc_start: 0.8213 (t80) cc_final: 0.7678 (t80) REVERT: A 397 PHE cc_start: 0.7761 (t80) cc_final: 0.7294 (t80) REVERT: A 414 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 432 MET cc_start: 0.8423 (tpt) cc_final: 0.8031 (tpt) REVERT: A 443 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 447 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8863 (mtmt) REVERT: A 454 VAL cc_start: 0.9121 (t) cc_final: 0.8790 (t) REVERT: A 458 LEU cc_start: 0.8885 (mt) cc_final: 0.8683 (mt) REVERT: A 459 LYS cc_start: 0.8307 (tppp) cc_final: 0.6438 (tppp) REVERT: A 463 MET cc_start: 0.7841 (mmp) cc_final: 0.6956 (mmp) REVERT: A 470 ARG cc_start: 0.7992 (ptt90) cc_final: 0.7420 (ptt-90) REVERT: A 473 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8398 (mtpt) REVERT: A 476 LYS cc_start: 0.8754 (mttm) cc_final: 0.8479 (mmtp) REVERT: A 477 THR cc_start: 0.8212 (p) cc_final: 0.7985 (p) REVERT: A 478 ASP cc_start: 0.8121 (m-30) cc_final: 0.7762 (m-30) REVERT: A 486 CYS cc_start: 0.8820 (t) cc_final: 0.8450 (p) REVERT: A 487 ILE cc_start: 0.8971 (mt) cc_final: 0.8633 (pt) REVERT: A 488 MET cc_start: 0.8176 (mmp) cc_final: 0.7964 (mmp) REVERT: A 496 LEU cc_start: 0.8935 (tp) cc_final: 0.8461 (tp) REVERT: A 503 LEU cc_start: 0.9277 (mt) cc_final: 0.9021 (mm) REVERT: A 536 TYR cc_start: 0.8345 (m-80) cc_final: 0.8090 (m-80) REVERT: A 537 LYS cc_start: 0.8710 (tttt) cc_final: 0.8383 (tttt) REVERT: A 549 ARG cc_start: 0.7844 (ttt90) cc_final: 0.7180 (ttm-80) REVERT: A 560 ASP cc_start: 0.8330 (m-30) cc_final: 0.7961 (m-30) REVERT: A 563 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8208 (mmmt) REVERT: A 564 LYS cc_start: 0.8967 (tppt) cc_final: 0.8446 (tppt) REVERT: A 567 ASN cc_start: 0.8378 (m-40) cc_final: 0.8031 (m110) REVERT: A 590 LYS cc_start: 0.8599 (pptt) cc_final: 0.8267 (tmmt) REVERT: A 678 MET cc_start: 0.8235 (mmm) cc_final: 0.8030 (mmm) REVERT: A 687 ASP cc_start: 0.8495 (t0) cc_final: 0.8125 (t0) REVERT: A 705 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7702 (tm-30) REVERT: A 717 ARG cc_start: 0.8173 (mpt-90) cc_final: 0.7871 (mtm180) REVERT: A 723 HIS cc_start: 0.8063 (t70) cc_final: 0.7728 (t70) REVERT: A 724 ASP cc_start: 0.8240 (m-30) cc_final: 0.7907 (m-30) REVERT: A 727 LEU cc_start: 0.8778 (mm) cc_final: 0.8122 (mt) REVERT: A 728 HIS cc_start: 0.8827 (t70) cc_final: 0.8577 (t-90) REVERT: A 731 ASN cc_start: 0.8496 (m110) cc_final: 0.8122 (m110) REVERT: B 32 PHE cc_start: 0.8343 (t80) cc_final: 0.8100 (t80) REVERT: B 33 GLN cc_start: 0.8453 (pp30) cc_final: 0.8133 (pp30) REVERT: B 37 GLU cc_start: 0.8397 (pp20) cc_final: 0.8129 (pp20) REVERT: B 38 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.8011 (tpp80) REVERT: B 105 TYR cc_start: 0.7364 (m-80) cc_final: 0.7003 (m-80) REVERT: B 122 PHE cc_start: 0.8383 (m-80) cc_final: 0.7822 (m-80) REVERT: B 124 ILE cc_start: 0.8776 (mm) cc_final: 0.8472 (mm) REVERT: B 125 LEU cc_start: 0.8908 (mt) cc_final: 0.8665 (tp) REVERT: B 137 SER cc_start: 0.8074 (t) cc_final: 0.7757 (t) REVERT: B 144 VAL cc_start: 0.8666 (p) cc_final: 0.8115 (m) REVERT: B 147 MET cc_start: 0.9078 (mtt) cc_final: 0.8722 (mtt) REVERT: B 186 VAL cc_start: 0.8977 (p) cc_final: 0.8611 (m) REVERT: B 203 PHE cc_start: 0.6838 (m-80) cc_final: 0.6332 (m-80) REVERT: B 213 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7306 (mtp180) REVERT: B 236 LEU cc_start: 0.8838 (tp) cc_final: 0.8612 (tp) REVERT: B 237 LYS cc_start: 0.9025 (pttt) cc_final: 0.8482 (pttp) REVERT: B 238 ILE cc_start: 0.8813 (tp) cc_final: 0.8454 (pt) REVERT: B 241 ASN cc_start: 0.8098 (m110) cc_final: 0.7347 (m110) REVERT: B 250 ILE cc_start: 0.8793 (pt) cc_final: 0.8430 (mm) REVERT: B 251 LEU cc_start: 0.8827 (mm) cc_final: 0.7251 (mm) REVERT: B 255 TYR cc_start: 0.7599 (m-10) cc_final: 0.7122 (m-80) REVERT: B 259 GLU cc_start: 0.8730 (tt0) cc_final: 0.8347 (tm-30) REVERT: B 260 ILE cc_start: 0.9214 (mm) cc_final: 0.8848 (mt) REVERT: B 261 PHE cc_start: 0.8281 (m-10) cc_final: 0.8013 (m-10) REVERT: B 276 LEU cc_start: 0.8784 (tp) cc_final: 0.8286 (mt) REVERT: B 279 ILE cc_start: 0.8638 (tp) cc_final: 0.8260 (pt) REVERT: B 286 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8713 (pttm) REVERT: B 303 GLU cc_start: 0.8950 (mp0) cc_final: 0.8627 (mp0) REVERT: B 318 ASN cc_start: 0.8486 (t0) cc_final: 0.8271 (t0) REVERT: B 322 ASN cc_start: 0.8090 (m110) cc_final: 0.7693 (t0) REVERT: B 323 TYR cc_start: 0.8130 (m-80) cc_final: 0.6863 (m-80) REVERT: B 432 MET cc_start: 0.8397 (ppp) cc_final: 0.8175 (ppp) REVERT: B 440 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7261 (ttp80) REVERT: B 459 LYS cc_start: 0.8755 (mmtt) cc_final: 0.7606 (mmtt) REVERT: B 463 MET cc_start: 0.7462 (mmm) cc_final: 0.6494 (mmm) REVERT: B 473 LYS cc_start: 0.8549 (mttp) cc_final: 0.7620 (pttm) REVERT: B 476 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7927 (mmmm) REVERT: B 484 PHE cc_start: 0.8401 (t80) cc_final: 0.7624 (t80) REVERT: B 488 MET cc_start: 0.7544 (tpp) cc_final: 0.6068 (tpp) REVERT: B 491 ILE cc_start: 0.8918 (mt) cc_final: 0.8660 (mm) REVERT: B 492 LEU cc_start: 0.8751 (mt) cc_final: 0.7293 (mt) REVERT: B 495 ASP cc_start: 0.7456 (p0) cc_final: 0.6977 (p0) REVERT: B 496 LEU cc_start: 0.7930 (mt) cc_final: 0.7130 (mt) REVERT: B 498 LEU cc_start: 0.8908 (tp) cc_final: 0.8674 (tp) REVERT: B 512 ARG cc_start: 0.8655 (mtm180) cc_final: 0.8044 (mtm110) REVERT: B 514 GLN cc_start: 0.8559 (tt0) cc_final: 0.8276 (tp40) REVERT: B 529 ILE cc_start: 0.8793 (mm) cc_final: 0.8570 (mm) REVERT: B 535 HIS cc_start: 0.7664 (m90) cc_final: 0.7430 (m90) REVERT: B 563 LYS cc_start: 0.8949 (tppt) cc_final: 0.8302 (tmtt) REVERT: B 564 LYS cc_start: 0.9257 (ttmm) cc_final: 0.9052 (ttmm) REVERT: B 567 ASN cc_start: 0.8275 (m-40) cc_final: 0.7604 (m-40) REVERT: B 577 VAL cc_start: 0.9040 (m) cc_final: 0.8735 (p) REVERT: B 580 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8436 (tptt) REVERT: B 586 ARG cc_start: 0.8393 (ppt170) cc_final: 0.8173 (ttp80) REVERT: B 656 HIS cc_start: 0.7041 (m90) cc_final: 0.6690 (m90) REVERT: B 666 SER cc_start: 0.8689 (p) cc_final: 0.8481 (p) REVERT: B 674 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8327 (ttm110) REVERT: B 677 ARG cc_start: 0.8329 (ttt180) cc_final: 0.7896 (ttm-80) REVERT: B 682 GLU cc_start: 0.7957 (tp30) cc_final: 0.7693 (tp30) REVERT: B 691 TYR cc_start: 0.7730 (m-80) cc_final: 0.7029 (m-80) REVERT: B 697 ASP cc_start: 0.5984 (t0) cc_final: 0.5773 (t0) REVERT: B 716 ASP cc_start: 0.8266 (p0) cc_final: 0.7994 (p0) REVERT: B 720 LEU cc_start: 0.9167 (mp) cc_final: 0.8842 (mt) REVERT: B 727 LEU cc_start: 0.8938 (mt) cc_final: 0.8535 (mt) REVERT: B 730 GLN cc_start: 0.8964 (tt0) cc_final: 0.8442 (pp30) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.2578 time to fit residues: 123.1558 Evaluate side-chains 331 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.110941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089401 restraints weight = 26263.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092582 restraints weight = 16154.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094961 restraints weight = 11116.301| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5633 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= 0.211 Angle : 0.643 9.801 14128 Z= 0.333 Chirality : 0.044 0.326 1716 Planarity : 0.004 0.055 1757 Dihedral : 4.296 24.104 1415 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1319 helix: 0.58 (0.18), residues: 832 sheet: -2.23 (0.99), residues: 28 loop : -2.17 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP B 482 HIS 0.003 0.001 HIS A 723 PHE 0.029 0.001 PHE B 203 TYR 0.019 0.002 TYR B 578 ARG 0.006 0.000 ARG B 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2881.66 seconds wall clock time: 52 minutes 2.98 seconds (3122.98 seconds total)