Starting phenix.real_space_refine on Mon Jun 9 04:13:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.map" model { file = "/net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wla_32579/06_2025/7wla_32579.cif" } resolution = 3.76 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6653 2.51 5 N 1687 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10193 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 6.37, per 1000 atoms: 0.62 Number of scatterers: 10193 At special positions: 0 Unit cell: (85.772, 127.612, 123.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1811 8.00 N 1687 7.00 C 6653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 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: 61 helices and 6 sheets defined 64.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.765A 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: 3.851A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.506A 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: 5.125A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.967A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.958A 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: 3.699A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.909A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.598A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.735A 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: 3.673A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.582A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.560A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.608A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.844A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.206A 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: 3.728A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.653A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.642A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.738A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.547A pdb=" N VAL A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.770A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.908A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.752A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.622A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.878A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.540A pdb=" N SER B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.546A pdb=" N LEU B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.716A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 removed outlier: 3.839A 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 225 through 240 removed outlier: 4.136A 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: 3.651A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 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: 4.130A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.525A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.578A pdb=" N GLU B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.525A pdb=" N LEU B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.651A pdb=" N ALA B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.885A pdb=" N ARG B 470 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.552A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.690A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.984A 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: 3.590A pdb=" N ASN B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.602A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 4.177A pdb=" N GLU B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.575A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.724A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.743A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.375A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 2247 1.46 - 1.58: 4872 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10395 Sorted by residual: bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.64e-01 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.45e-01 bond pdb=" C GLU B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.08e-01 bond pdb=" CA PHE A 122 " pdb=" C PHE A 122 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.14e-02 7.69e+03 6.08e-01 bond pdb=" N PRO B 337 " pdb=" CA PRO B 337 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 5.47e-01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13736 1.09 - 2.19: 298 2.19 - 3.28: 64 3.28 - 4.38: 19 4.38 - 5.47: 11 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 114.56 111.18 3.38 1.27e+00 6.20e-01 7.09e+00 angle pdb=" C PHE A 121 " pdb=" N PHE A 122 " pdb=" CA PHE A 122 " ideal model delta sigma weight residual 119.78 122.74 -2.96 1.24e+00 6.50e-01 5.72e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.74 -4.40 2.08e+00 2.31e-01 4.47e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 125.76 -3.79 1.80e+00 3.09e-01 4.43e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 121.54 125.51 -3.97 1.91e+00 2.74e-01 4.32e+00 ... (remaining 14123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5965 17.76 - 35.51: 179 35.51 - 53.27: 32 53.27 - 71.03: 0 71.03 - 88.79: 4 Dihedral angle restraints: 6180 sinusoidal: 2353 harmonic: 3827 Sorted by residual: 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 86.02 -86.02 1 3.00e+01 1.11e-03 9.93e+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 -128.09 -51.91 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N ARG A 36 " pdb=" CA ARG A 36 " pdb=" CB ARG A 36 " pdb=" CG ARG A 36 " ideal model delta sinusoidal sigma weight residual -180.00 -128.25 -51.75 3 1.50e+01 4.44e-03 9.05e+00 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 957 0.026 - 0.052: 503 0.052 - 0.078: 177 0.078 - 0.104: 62 0.104 - 0.130: 17 Chirality restraints: 1716 Sorted by residual: 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 4.21e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-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 4.27e-02 2.91e+00 pdb=" N PRO B 76 " -0.074 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 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 553 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 654 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.018 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 705 2.74 - 3.28: 11232 3.28 - 3.82: 16750 3.82 - 4.36: 19648 4.36 - 4.90: 33038 Nonbonded interactions: 81373 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.225 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.242 3.120 ... (remaining 81368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 0.043 10395 Z= 0.091 Angle : 0.445 5.469 14128 Z= 0.251 Chirality : 0.037 0.130 1716 Planarity : 0.003 0.043 1757 Dihedral : 8.816 88.787 3714 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.01 % Allowed : 5.52 % Favored : 90.47 % 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: -4.06 (0.19), residues: 1319 helix: -2.14 (0.15), residues: 815 sheet: -3.23 (0.68), residues: 30 loop : -3.49 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 83 HIS 0.001 0.000 HIS A 723 PHE 0.008 0.001 PHE A 555 TYR 0.005 0.001 TYR A 377 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.23262 ( 544) hydrogen bonds : angle 6.79140 ( 1593) covalent geometry : bond 0.00169 (10395) covalent geometry : angle 0.44482 (14128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7066 (mmt90) REVERT: A 93 SER cc_start: 0.8253 (t) cc_final: 0.7920 (p) REVERT: A 122 PHE cc_start: 0.7110 (m-80) cc_final: 0.6612 (m-10) REVERT: A 195 LEU cc_start: 0.8547 (tp) cc_final: 0.7962 (tp) REVERT: A 199 ILE cc_start: 0.8218 (mt) cc_final: 0.7783 (mt) REVERT: A 206 LEU cc_start: 0.7834 (mt) cc_final: 0.7563 (mt) REVERT: A 213 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7195 (mtm-85) REVERT: A 231 VAL cc_start: 0.8650 (t) cc_final: 0.7990 (p) REVERT: A 235 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7666 (mm-40) REVERT: A 237 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7839 (ttpp) REVERT: A 238 ILE cc_start: 0.8539 (mt) cc_final: 0.8339 (tp) REVERT: A 260 ILE cc_start: 0.8844 (mt) cc_final: 0.8503 (tp) REVERT: A 272 PHE cc_start: 0.7779 (t80) cc_final: 0.7542 (t80) REVERT: A 280 ILE cc_start: 0.8880 (mt) cc_final: 0.8622 (tp) REVERT: A 286 LYS cc_start: 0.9159 (tppt) cc_final: 0.8796 (mmmm) REVERT: A 355 SER cc_start: 0.7752 (m) cc_final: 0.7495 (p) REVERT: A 384 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5550 (mm-30) REVERT: A 398 PHE cc_start: 0.7104 (m-80) cc_final: 0.6473 (m-10) REVERT: A 432 MET cc_start: 0.7370 (tpt) cc_final: 0.6650 (tpt) REVERT: A 473 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7502 (mtpt) REVERT: A 484 PHE cc_start: 0.8200 (t80) cc_final: 0.7761 (t80) REVERT: A 488 MET cc_start: 0.7136 (tpp) cc_final: 0.6686 (tpp) REVERT: A 512 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: A 546 LYS cc_start: 0.8240 (tptm) cc_final: 0.7857 (tptm) REVERT: A 564 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8221 (ttmm) REVERT: A 676 LEU cc_start: 0.8143 (mt) cc_final: 0.7890 (tp) REVERT: A 681 LYS cc_start: 0.7819 (tptt) cc_final: 0.6864 (tptt) REVERT: A 686 ILE cc_start: 0.8389 (pt) cc_final: 0.7896 (mm) REVERT: A 687 ASP cc_start: 0.6664 (t0) cc_final: 0.6180 (t0) REVERT: A 723 HIS cc_start: 0.7182 (t-170) cc_final: 0.6781 (t-90) REVERT: B 48 ASP cc_start: 0.6066 (p0) cc_final: 0.5755 (m-30) REVERT: B 118 TYR cc_start: 0.6964 (m-10) cc_final: 0.6603 (m-80) REVERT: B 137 SER cc_start: 0.8017 (t) cc_final: 0.7779 (p) REVERT: B 151 VAL cc_start: 0.7229 (m) cc_final: 0.6544 (p) REVERT: B 195 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5859 (tp) REVERT: B 199 ILE cc_start: 0.7579 (mp) cc_final: 0.7350 (mp) REVERT: B 231 VAL cc_start: 0.8453 (p) cc_final: 0.7928 (p) REVERT: B 232 LEU cc_start: 0.8370 (tp) cc_final: 0.8116 (tt) REVERT: B 235 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7169 (mm-40) REVERT: B 238 ILE cc_start: 0.8276 (tp) cc_final: 0.8035 (mt) REVERT: B 244 THR cc_start: 0.6562 (t) cc_final: 0.6358 (p) REVERT: B 251 LEU cc_start: 0.8599 (mm) cc_final: 0.6964 (mm) REVERT: B 255 TYR cc_start: 0.8066 (m-10) cc_final: 0.7567 (m-80) REVERT: B 260 ILE cc_start: 0.9166 (mt) cc_final: 0.8938 (tp) REVERT: B 262 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7242 (tp-100) REVERT: B 286 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7316 (ttmm) REVERT: B 293 LYS cc_start: 0.8550 (pptt) cc_final: 0.8230 (pptt) REVERT: B 309 ILE cc_start: 0.8849 (pt) cc_final: 0.8511 (mm) REVERT: B 320 GLU cc_start: 0.7648 (tp30) cc_final: 0.7428 (tp30) REVERT: B 371 TYR cc_start: 0.7105 (m-80) cc_final: 0.6726 (m-80) REVERT: B 375 HIS cc_start: 0.6369 (t-90) cc_final: 0.6065 (t-90) REVERT: B 426 ILE cc_start: 0.8357 (tp) cc_final: 0.8116 (pt) REVERT: B 473 LYS cc_start: 0.7903 (mttp) cc_final: 0.6765 (mttp) REVERT: B 475 ASN cc_start: 0.7784 (t0) cc_final: 0.7357 (t0) REVERT: B 483 VAL cc_start: 0.8716 (p) cc_final: 0.8459 (t) REVERT: B 487 ILE cc_start: 0.8462 (pt) cc_final: 0.8142 (mp) REVERT: B 488 MET cc_start: 0.6912 (tpp) cc_final: 0.5808 (tpp) REVERT: B 492 LEU cc_start: 0.8447 (mt) cc_final: 0.7570 (mt) REVERT: B 515 PHE cc_start: 0.8051 (m-80) cc_final: 0.7396 (m-80) REVERT: B 580 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7920 (mmmt) REVERT: B 583 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8374 (tttm) REVERT: B 677 ARG cc_start: 0.7336 (ttt180) cc_final: 0.7098 (ttp80) REVERT: B 682 GLU cc_start: 0.7805 (tp30) cc_final: 0.7533 (tp30) REVERT: B 695 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.4754 (mp) REVERT: B 701 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 705 GLN cc_start: 0.8165 (tt0) cc_final: 0.7898 (tt0) REVERT: B 706 CYS cc_start: 0.7461 (m) cc_final: 0.6640 (m) outliers start: 45 outliers final: 19 residues processed: 413 average time/residue: 0.2679 time to fit residues: 147.6749 Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 114 GLN A 135 HIS A 246 ASN A 289 ASN A 413 GLN A 514 GLN A 519 ASN A 567 ASN A 728 HIS A 730 GLN A 732 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN B 383 GLN B 446 GLN B 457 ASN B 474 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 689 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119352 restraints weight = 20351.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123280 restraints weight = 11396.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125873 restraints weight = 7224.316| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10395 Z= 0.191 Angle : 0.630 7.319 14128 Z= 0.330 Chirality : 0.043 0.215 1716 Planarity : 0.005 0.047 1757 Dihedral : 5.840 80.226 1458 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.72 % Allowed : 14.25 % Favored : 81.03 % 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: -2.30 (0.21), residues: 1319 helix: -0.62 (0.17), residues: 812 sheet: -2.97 (0.79), residues: 32 loop : -2.97 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.004 0.001 HIS B 728 PHE 0.017 0.001 PHE B 229 TYR 0.022 0.002 TYR A 556 ARG 0.011 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 544) hydrogen bonds : angle 4.27140 ( 1593) covalent geometry : bond 0.00403 (10395) covalent geometry : angle 0.62968 (14128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7654 (tpp-160) cc_final: 0.7311 (mmt90) REVERT: A 93 SER cc_start: 0.8517 (t) cc_final: 0.8112 (p) REVERT: A 122 PHE cc_start: 0.7320 (m-80) cc_final: 0.6841 (m-10) REVERT: A 123 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.8156 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8520 (tp) cc_final: 0.7951 (tp) REVERT: A 199 ILE cc_start: 0.8202 (mt) cc_final: 0.7868 (mt) REVERT: A 231 VAL cc_start: 0.8734 (t) cc_final: 0.8003 (p) REVERT: A 235 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7677 (mm-40) REVERT: A 237 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8016 (ttpp) REVERT: A 247 TYR cc_start: 0.7418 (m-10) cc_final: 0.6307 (m-10) REVERT: A 272 PHE cc_start: 0.7958 (t80) cc_final: 0.7403 (t80) REVERT: A 280 ILE cc_start: 0.8963 (mt) cc_final: 0.8746 (tp) REVERT: A 286 LYS cc_start: 0.9169 (tppt) cc_final: 0.8770 (mmmm) REVERT: A 355 SER cc_start: 0.7872 (m) cc_final: 0.7559 (p) REVERT: A 384 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6031 (mm-30) REVERT: A 395 SER cc_start: 0.8615 (m) cc_final: 0.8282 (p) REVERT: A 398 PHE cc_start: 0.7158 (m-80) cc_final: 0.6480 (m-10) REVERT: A 432 MET cc_start: 0.7423 (tpt) cc_final: 0.6785 (tpt) REVERT: A 443 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6988 (pp20) REVERT: A 473 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7950 (mtpt) REVERT: A 484 PHE cc_start: 0.8327 (t80) cc_final: 0.7933 (t80) REVERT: A 488 MET cc_start: 0.7559 (tpp) cc_final: 0.7080 (tpp) REVERT: A 512 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8398 (mtm-85) REVERT: A 530 TYR cc_start: 0.7288 (m-80) cc_final: 0.7029 (m-80) REVERT: A 546 LYS cc_start: 0.8269 (tptm) cc_final: 0.7768 (tptm) REVERT: A 549 ARG cc_start: 0.6963 (ttt90) cc_final: 0.6719 (ttm-80) REVERT: A 556 TYR cc_start: 0.8153 (p90) cc_final: 0.7797 (p90) REVERT: A 560 ASP cc_start: 0.8189 (m-30) cc_final: 0.7931 (t0) REVERT: A 563 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7952 (ttmm) REVERT: A 662 CYS cc_start: 0.7952 (m) cc_final: 0.7528 (m) REVERT: A 686 ILE cc_start: 0.8630 (pt) cc_final: 0.8364 (mm) REVERT: A 687 ASP cc_start: 0.6846 (t0) cc_final: 0.6431 (t0) REVERT: A 723 HIS cc_start: 0.7145 (t-170) cc_final: 0.6868 (t-90) REVERT: B 29 GLU cc_start: 0.6817 (mp0) cc_final: 0.6558 (mp0) REVERT: B 118 TYR cc_start: 0.7150 (m-10) cc_final: 0.6790 (m-80) REVERT: B 195 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6254 (tp) REVERT: B 199 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 207 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 230 GLN cc_start: 0.7916 (tp40) cc_final: 0.7329 (tm-30) REVERT: B 231 VAL cc_start: 0.8664 (p) cc_final: 0.7894 (p) REVERT: B 235 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7268 (mm-40) REVERT: B 236 LEU cc_start: 0.8058 (tp) cc_final: 0.7694 (tp) REVERT: B 237 LYS cc_start: 0.8245 (pttt) cc_final: 0.7741 (pttt) REVERT: B 251 LEU cc_start: 0.8425 (mm) cc_final: 0.6749 (mm) REVERT: B 255 TYR cc_start: 0.8240 (m-10) cc_final: 0.7701 (m-80) REVERT: B 259 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 263 ASN cc_start: 0.7384 (t0) cc_final: 0.6987 (t0) REVERT: B 271 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7634 (p0) REVERT: B 286 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7996 (ttmm) REVERT: B 293 LYS cc_start: 0.8580 (pptt) cc_final: 0.8253 (tppt) REVERT: B 309 ILE cc_start: 0.8858 (pt) cc_final: 0.8654 (mm) REVERT: B 320 GLU cc_start: 0.7638 (tp30) cc_final: 0.7293 (tp30) REVERT: B 359 VAL cc_start: 0.7859 (p) cc_final: 0.7518 (m) REVERT: B 395 SER cc_start: 0.7588 (m) cc_final: 0.7057 (p) REVERT: B 475 ASN cc_start: 0.7873 (t0) cc_final: 0.7508 (t0) REVERT: B 487 ILE cc_start: 0.8602 (pt) cc_final: 0.8120 (mm) REVERT: B 488 MET cc_start: 0.7192 (tpp) cc_final: 0.6000 (tpp) REVERT: B 492 LEU cc_start: 0.8552 (mt) cc_final: 0.7747 (mt) REVERT: B 499 LEU cc_start: 0.8284 (tp) cc_final: 0.8027 (tp) REVERT: B 560 ASP cc_start: 0.8004 (p0) cc_final: 0.7758 (p0) REVERT: B 583 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8467 (tttm) REVERT: B 677 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7073 (ttp80) REVERT: B 682 GLU cc_start: 0.8009 (tp30) cc_final: 0.7755 (tp30) REVERT: B 701 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6949 (mm-30) REVERT: B 702 LYS cc_start: 0.7182 (tttm) cc_final: 0.6239 (tptp) REVERT: B 706 CYS cc_start: 0.7352 (m) cc_final: 0.5851 (m) outliers start: 53 outliers final: 32 residues processed: 348 average time/residue: 0.2517 time to fit residues: 118.1680 Evaluate side-chains 326 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 0.0570 chunk 115 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 383 GLN A 567 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116838 restraints weight = 20655.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120782 restraints weight = 11590.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.123424 restraints weight = 7263.408| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10395 Z= 0.170 Angle : 0.626 8.513 14128 Z= 0.326 Chirality : 0.043 0.198 1716 Planarity : 0.004 0.050 1757 Dihedral : 5.748 81.011 1450 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.81 % Allowed : 17.10 % Favored : 78.09 % 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: -1.68 (0.22), residues: 1319 helix: -0.11 (0.18), residues: 806 sheet: -2.41 (0.91), residues: 32 loop : -2.75 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.002 0.001 HIS A 728 PHE 0.024 0.001 PHE A 719 TYR 0.020 0.002 TYR A 556 ARG 0.003 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 544) hydrogen bonds : angle 4.14361 ( 1593) covalent geometry : bond 0.00366 (10395) covalent geometry : angle 0.62606 (14128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7738 (mm110) cc_final: 0.7431 (mm110) REVERT: A 36 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7248 (mmt90) REVERT: A 37 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: A 93 SER cc_start: 0.8487 (t) cc_final: 0.8134 (p) REVERT: A 122 PHE cc_start: 0.7309 (m-80) cc_final: 0.6800 (m-10) REVERT: A 123 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8533 (tp) cc_final: 0.7954 (tp) REVERT: A 199 ILE cc_start: 0.8213 (mt) cc_final: 0.7875 (mt) REVERT: A 231 VAL cc_start: 0.8763 (t) cc_final: 0.8169 (p) REVERT: A 235 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7847 (mm-40) REVERT: A 237 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8011 (ttpp) REVERT: A 247 TYR cc_start: 0.7355 (m-10) cc_final: 0.6908 (m-10) REVERT: A 280 ILE cc_start: 0.8997 (mt) cc_final: 0.8753 (tp) REVERT: A 286 LYS cc_start: 0.9184 (tppt) cc_final: 0.8841 (mmmm) REVERT: A 355 SER cc_start: 0.7881 (m) cc_final: 0.7562 (p) REVERT: A 371 TYR cc_start: 0.8015 (m-80) cc_final: 0.7674 (m-80) REVERT: A 383 GLN cc_start: 0.7642 (mt0) cc_final: 0.7360 (mt0) REVERT: A 384 GLU cc_start: 0.6789 (mm-30) cc_final: 0.5956 (mm-30) REVERT: A 395 SER cc_start: 0.8617 (m) cc_final: 0.8074 (p) REVERT: A 398 PHE cc_start: 0.7158 (m-80) cc_final: 0.6489 (m-10) REVERT: A 432 MET cc_start: 0.7538 (tpt) cc_final: 0.7274 (tpt) REVERT: A 447 LYS cc_start: 0.8515 (mtpt) cc_final: 0.7980 (mttp) REVERT: A 473 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7993 (mtpt) REVERT: A 476 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8460 (mtpp) REVERT: A 478 ASP cc_start: 0.8405 (t0) cc_final: 0.7871 (t0) REVERT: A 484 PHE cc_start: 0.8355 (t80) cc_final: 0.7988 (t80) REVERT: A 488 MET cc_start: 0.7686 (tpp) cc_final: 0.7175 (tpp) REVERT: A 530 TYR cc_start: 0.7407 (m-80) cc_final: 0.7110 (m-80) REVERT: A 546 LYS cc_start: 0.8276 (tptm) cc_final: 0.7744 (tptm) REVERT: A 556 TYR cc_start: 0.8175 (p90) cc_final: 0.7865 (p90) REVERT: A 560 ASP cc_start: 0.8195 (m-30) cc_final: 0.7937 (t0) REVERT: A 563 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8096 (ttmm) REVERT: A 662 CYS cc_start: 0.7971 (m) cc_final: 0.7594 (m) REVERT: A 686 ILE cc_start: 0.8680 (pt) cc_final: 0.8434 (mm) REVERT: A 687 ASP cc_start: 0.6939 (t0) cc_final: 0.6507 (t0) REVERT: A 698 ASP cc_start: 0.7686 (t0) cc_final: 0.7462 (t0) REVERT: A 715 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7192 (mmmm) REVERT: B 29 GLU cc_start: 0.7058 (mp0) cc_final: 0.6829 (mp0) REVERT: B 103 MET cc_start: 0.6183 (mmt) cc_final: 0.5921 (mmt) REVERT: B 118 TYR cc_start: 0.7202 (m-10) cc_final: 0.6950 (m-80) REVERT: B 134 ARG cc_start: 0.6411 (mtt90) cc_final: 0.6184 (mtt90) REVERT: B 195 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6371 (tp) REVERT: B 199 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 207 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 213 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7842 (mtm180) REVERT: B 230 GLN cc_start: 0.7956 (tp40) cc_final: 0.7399 (tm-30) REVERT: B 231 VAL cc_start: 0.8650 (p) cc_final: 0.7889 (p) REVERT: B 235 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7319 (mm-40) REVERT: B 236 LEU cc_start: 0.8129 (tp) cc_final: 0.7780 (tp) REVERT: B 237 LYS cc_start: 0.8276 (pttt) cc_final: 0.7748 (pttp) REVERT: B 251 LEU cc_start: 0.8406 (mm) cc_final: 0.6530 (mm) REVERT: B 255 TYR cc_start: 0.8271 (m-10) cc_final: 0.7686 (m-80) REVERT: B 259 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 263 ASN cc_start: 0.7573 (t0) cc_final: 0.7143 (t0) REVERT: B 271 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7236 (p0) REVERT: B 286 LYS cc_start: 0.8278 (ttmm) cc_final: 0.8023 (mmmm) REVERT: B 293 LYS cc_start: 0.8599 (pptt) cc_final: 0.7995 (mmmm) REVERT: B 320 GLU cc_start: 0.7784 (tp30) cc_final: 0.7433 (tp30) REVERT: B 359 VAL cc_start: 0.7876 (p) cc_final: 0.7351 (t) REVERT: B 395 SER cc_start: 0.7628 (m) cc_final: 0.7106 (p) REVERT: B 473 LYS cc_start: 0.8021 (mttp) cc_final: 0.7008 (mtpp) REVERT: B 487 ILE cc_start: 0.8581 (pt) cc_final: 0.8340 (mt) REVERT: B 488 MET cc_start: 0.7233 (tpp) cc_final: 0.5851 (tpp) REVERT: B 492 LEU cc_start: 0.8614 (mt) cc_final: 0.7690 (mt) REVERT: B 499 LEU cc_start: 0.8268 (tp) cc_final: 0.8037 (tp) REVERT: B 502 LEU cc_start: 0.7909 (tp) cc_final: 0.7558 (mt) REVERT: B 503 LEU cc_start: 0.8144 (mm) cc_final: 0.7816 (mp) REVERT: B 677 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7099 (ttp80) REVERT: B 682 GLU cc_start: 0.8256 (tp30) cc_final: 0.7744 (tp30) REVERT: B 685 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7556 (ptp90) REVERT: B 687 ASP cc_start: 0.6892 (t0) cc_final: 0.6497 (t0) REVERT: B 701 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6942 (mm-30) REVERT: B 706 CYS cc_start: 0.7363 (m) cc_final: 0.7103 (m) outliers start: 54 outliers final: 34 residues processed: 339 average time/residue: 0.2664 time to fit residues: 124.1950 Evaluate side-chains 329 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 34 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117212 restraints weight = 20395.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121101 restraints weight = 11509.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123677 restraints weight = 7302.406| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10395 Z= 0.138 Angle : 0.610 10.159 14128 Z= 0.314 Chirality : 0.043 0.406 1716 Planarity : 0.004 0.055 1757 Dihedral : 5.779 82.544 1450 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.99 % Allowed : 19.15 % Favored : 75.87 % 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: -1.46 (0.23), residues: 1319 helix: 0.04 (0.18), residues: 835 sheet: -2.21 (0.93), residues: 32 loop : -2.79 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.016 0.001 PHE A 385 TYR 0.023 0.001 TYR A 105 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 544) hydrogen bonds : angle 4.02865 ( 1593) covalent geometry : bond 0.00300 (10395) covalent geometry : angle 0.60990 (14128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7660 (mm110) cc_final: 0.7437 (mm110) REVERT: A 36 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7372 (mmt90) REVERT: A 37 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: A 93 SER cc_start: 0.8503 (t) cc_final: 0.8122 (p) REVERT: A 105 TYR cc_start: 0.7515 (m-80) cc_final: 0.7266 (m-80) REVERT: A 122 PHE cc_start: 0.7286 (m-80) cc_final: 0.6826 (m-10) REVERT: A 123 PRO cc_start: 0.8296 (Cg_exo) cc_final: 0.8043 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8509 (tp) cc_final: 0.7973 (tp) REVERT: A 199 ILE cc_start: 0.8210 (mt) cc_final: 0.7859 (mt) REVERT: A 213 ARG cc_start: 0.7571 (mtm180) cc_final: 0.7365 (mtm-85) REVERT: A 231 VAL cc_start: 0.8760 (t) cc_final: 0.8141 (p) REVERT: A 235 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 237 LYS cc_start: 0.8362 (ttpp) cc_final: 0.7966 (ttpp) REVERT: A 259 GLU cc_start: 0.8186 (tt0) cc_final: 0.7927 (tt0) REVERT: A 271 ASP cc_start: 0.7401 (t0) cc_final: 0.7166 (m-30) REVERT: A 279 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8733 (mm) REVERT: A 280 ILE cc_start: 0.8966 (mt) cc_final: 0.8735 (tp) REVERT: A 286 LYS cc_start: 0.9204 (tppt) cc_final: 0.8843 (mmmm) REVERT: A 355 SER cc_start: 0.7876 (m) cc_final: 0.7586 (p) REVERT: A 383 GLN cc_start: 0.7545 (mt0) cc_final: 0.7258 (mt0) REVERT: A 384 GLU cc_start: 0.6736 (mm-30) cc_final: 0.5928 (mm-30) REVERT: A 395 SER cc_start: 0.8449 (m) cc_final: 0.8086 (p) REVERT: A 398 PHE cc_start: 0.7061 (m-80) cc_final: 0.6576 (m-10) REVERT: A 432 MET cc_start: 0.7458 (tpt) cc_final: 0.7105 (tpt) REVERT: A 447 LYS cc_start: 0.8443 (mtpt) cc_final: 0.7930 (mttp) REVERT: A 457 ASN cc_start: 0.8086 (m110) cc_final: 0.7577 (m110) REVERT: A 473 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8012 (mtpt) REVERT: A 476 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8467 (mtpp) REVERT: A 478 ASP cc_start: 0.8254 (t0) cc_final: 0.7690 (t0) REVERT: A 484 PHE cc_start: 0.8278 (t80) cc_final: 0.7940 (t80) REVERT: A 488 MET cc_start: 0.7616 (tpp) cc_final: 0.7143 (tpp) REVERT: A 511 LEU cc_start: 0.8836 (mt) cc_final: 0.8616 (mt) REVERT: A 530 TYR cc_start: 0.7399 (m-80) cc_final: 0.7138 (m-80) REVERT: A 546 LYS cc_start: 0.8278 (tptm) cc_final: 0.7760 (tptm) REVERT: A 556 TYR cc_start: 0.8221 (p90) cc_final: 0.7983 (p90) REVERT: A 560 ASP cc_start: 0.8125 (m-30) cc_final: 0.7882 (t0) REVERT: A 563 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8260 (ttmm) REVERT: A 662 CYS cc_start: 0.7930 (m) cc_final: 0.7596 (m) REVERT: A 686 ILE cc_start: 0.8743 (pt) cc_final: 0.8435 (mm) REVERT: A 687 ASP cc_start: 0.6882 (t0) cc_final: 0.6447 (t0) REVERT: A 694 LEU cc_start: 0.8371 (mm) cc_final: 0.8098 (mm) REVERT: A 705 GLN cc_start: 0.8043 (pt0) cc_final: 0.7780 (tt0) REVERT: A 715 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7154 (mmmm) REVERT: B 103 MET cc_start: 0.5819 (mmt) cc_final: 0.5560 (mmp) REVERT: B 118 TYR cc_start: 0.7140 (m-10) cc_final: 0.6878 (m-80) REVERT: B 134 ARG cc_start: 0.6548 (mtt90) cc_final: 0.6345 (mtt90) REVERT: B 158 ASP cc_start: 0.5225 (m-30) cc_final: 0.3667 (m-30) REVERT: B 185 ARG cc_start: 0.6920 (mmt180) cc_final: 0.5744 (mmt180) REVERT: B 192 LEU cc_start: 0.8601 (tp) cc_final: 0.8160 (pp) REVERT: B 195 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6363 (tp) REVERT: B 199 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 207 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 230 GLN cc_start: 0.7841 (tp40) cc_final: 0.7249 (tm-30) REVERT: B 231 VAL cc_start: 0.8652 (p) cc_final: 0.7818 (p) REVERT: B 235 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7259 (mm-40) REVERT: B 236 LEU cc_start: 0.8081 (tp) cc_final: 0.7678 (tp) REVERT: B 237 LYS cc_start: 0.8239 (pttt) cc_final: 0.7810 (pttt) REVERT: B 251 LEU cc_start: 0.8459 (mm) cc_final: 0.6615 (mm) REVERT: B 255 TYR cc_start: 0.8205 (m-10) cc_final: 0.7650 (m-80) REVERT: B 259 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 263 ASN cc_start: 0.7462 (t0) cc_final: 0.6985 (t0) REVERT: B 286 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7800 (tppp) REVERT: B 293 LYS cc_start: 0.8587 (pptt) cc_final: 0.8019 (mmmm) REVERT: B 320 GLU cc_start: 0.7682 (tp30) cc_final: 0.7382 (tp30) REVERT: B 324 ASN cc_start: 0.7616 (t0) cc_final: 0.7241 (t0) REVERT: B 359 VAL cc_start: 0.7892 (p) cc_final: 0.7413 (t) REVERT: B 395 SER cc_start: 0.7753 (m) cc_final: 0.7231 (p) REVERT: B 473 LYS cc_start: 0.7904 (mttp) cc_final: 0.7058 (mtpp) REVERT: B 484 PHE cc_start: 0.8490 (t80) cc_final: 0.8289 (t80) REVERT: B 487 ILE cc_start: 0.8591 (pt) cc_final: 0.8385 (mt) REVERT: B 488 MET cc_start: 0.7131 (tpp) cc_final: 0.5857 (tpp) REVERT: B 492 LEU cc_start: 0.8624 (mt) cc_final: 0.7719 (mt) REVERT: B 499 LEU cc_start: 0.8289 (tp) cc_final: 0.8007 (tp) REVERT: B 502 LEU cc_start: 0.7987 (tp) cc_final: 0.7668 (mt) REVERT: B 580 LYS cc_start: 0.8235 (mmmt) cc_final: 0.8031 (mmmm) REVERT: B 677 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7044 (ttp80) REVERT: B 682 GLU cc_start: 0.8274 (tp30) cc_final: 0.7888 (tp30) REVERT: B 686 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 687 ASP cc_start: 0.6854 (t0) cc_final: 0.6518 (t0) outliers start: 56 outliers final: 36 residues processed: 332 average time/residue: 0.3874 time to fit residues: 179.8956 Evaluate side-chains 337 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 296 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS A 728 HIS A 732 GLN B 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.133888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.114836 restraints weight = 20310.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118614 restraints weight = 11502.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120987 restraints weight = 7322.108| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.169 Angle : 0.635 9.668 14128 Z= 0.329 Chirality : 0.044 0.244 1716 Planarity : 0.004 0.056 1757 Dihedral : 5.934 84.408 1450 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.72 % Allowed : 20.84 % Favored : 74.44 % 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: -1.27 (0.23), residues: 1319 helix: 0.19 (0.18), residues: 823 sheet: -2.50 (0.89), residues: 34 loop : -2.61 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.006 0.001 HIS A 723 PHE 0.017 0.001 PHE A 385 TYR 0.015 0.002 TYR A 556 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 544) hydrogen bonds : angle 4.00476 ( 1593) covalent geometry : bond 0.00352 (10395) covalent geometry : angle 0.63475 (14128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.086 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 36 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7587 (mmt90) REVERT: A 37 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: A 93 SER cc_start: 0.8506 (t) cc_final: 0.8157 (p) REVERT: A 122 PHE cc_start: 0.7302 (m-80) cc_final: 0.6861 (m-10) REVERT: A 123 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.8094 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8561 (tp) cc_final: 0.8049 (tp) REVERT: A 199 ILE cc_start: 0.8230 (mt) cc_final: 0.7892 (mt) REVERT: A 213 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7367 (mtm-85) REVERT: A 231 VAL cc_start: 0.8790 (t) cc_final: 0.8120 (p) REVERT: A 234 SER cc_start: 0.8817 (m) cc_final: 0.8366 (t) REVERT: A 235 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 237 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8108 (ttpp) REVERT: A 280 ILE cc_start: 0.8985 (mt) cc_final: 0.8756 (tp) REVERT: A 286 LYS cc_start: 0.9189 (tppt) cc_final: 0.8838 (mmmm) REVERT: A 355 SER cc_start: 0.7914 (m) cc_final: 0.7611 (p) REVERT: A 383 GLN cc_start: 0.7545 (mt0) cc_final: 0.7191 (mt0) REVERT: A 384 GLU cc_start: 0.6750 (mm-30) cc_final: 0.5962 (mm-30) REVERT: A 395 SER cc_start: 0.8455 (m) cc_final: 0.8087 (p) REVERT: A 398 PHE cc_start: 0.7093 (m-80) cc_final: 0.6557 (m-80) REVERT: A 447 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7928 (mttp) REVERT: A 457 ASN cc_start: 0.8193 (m110) cc_final: 0.7693 (m110) REVERT: A 467 ASP cc_start: 0.7623 (m-30) cc_final: 0.7354 (m-30) REVERT: A 473 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8033 (mtpt) REVERT: A 476 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8558 (mtpp) REVERT: A 478 ASP cc_start: 0.8161 (t0) cc_final: 0.7621 (t0) REVERT: A 484 PHE cc_start: 0.8277 (t80) cc_final: 0.7936 (t80) REVERT: A 488 MET cc_start: 0.7657 (tpp) cc_final: 0.7172 (tpp) REVERT: A 512 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8201 (mtt90) REVERT: A 530 TYR cc_start: 0.7492 (m-80) cc_final: 0.7207 (m-80) REVERT: A 546 LYS cc_start: 0.8253 (tptm) cc_final: 0.7732 (tptm) REVERT: A 662 CYS cc_start: 0.7863 (m) cc_final: 0.7602 (m) REVERT: A 686 ILE cc_start: 0.8779 (pt) cc_final: 0.8433 (mm) REVERT: A 687 ASP cc_start: 0.7101 (t0) cc_final: 0.6645 (t0) REVERT: A 694 LEU cc_start: 0.8376 (mm) cc_final: 0.8115 (mm) REVERT: A 698 ASP cc_start: 0.7625 (t0) cc_final: 0.7421 (t0) REVERT: A 715 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7120 (mmmm) REVERT: A 716 ASP cc_start: 0.7242 (t0) cc_final: 0.6910 (t0) REVERT: A 723 HIS cc_start: 0.7264 (t-90) cc_final: 0.6883 (t-90) REVERT: B 29 GLU cc_start: 0.7040 (mp0) cc_final: 0.6787 (mp0) REVERT: B 68 LEU cc_start: 0.8402 (mm) cc_final: 0.8120 (mt) REVERT: B 118 TYR cc_start: 0.7204 (m-10) cc_final: 0.6951 (m-80) REVERT: B 134 ARG cc_start: 0.6518 (mtt90) cc_final: 0.6279 (mtt90) REVERT: B 158 ASP cc_start: 0.5342 (m-30) cc_final: 0.5123 (m-30) REVERT: B 192 LEU cc_start: 0.8566 (tp) cc_final: 0.8161 (pp) REVERT: B 195 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6418 (tp) REVERT: B 199 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 207 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 213 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7871 (mtm180) REVERT: B 230 GLN cc_start: 0.7864 (tp40) cc_final: 0.7271 (tm-30) REVERT: B 231 VAL cc_start: 0.8655 (p) cc_final: 0.8174 (p) REVERT: B 236 LEU cc_start: 0.8088 (tp) cc_final: 0.7679 (tp) REVERT: B 237 LYS cc_start: 0.8248 (pttt) cc_final: 0.7733 (pttp) REVERT: B 251 LEU cc_start: 0.8488 (mm) cc_final: 0.6565 (mm) REVERT: B 255 TYR cc_start: 0.8203 (m-10) cc_final: 0.7682 (m-80) REVERT: B 259 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 263 ASN cc_start: 0.7451 (t0) cc_final: 0.6942 (t0) REVERT: B 286 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7831 (tppp) REVERT: B 320 GLU cc_start: 0.7727 (tp30) cc_final: 0.7433 (tp30) REVERT: B 349 MET cc_start: 0.6894 (mmm) cc_final: 0.6506 (mmp) REVERT: B 395 SER cc_start: 0.7845 (m) cc_final: 0.7283 (p) REVERT: B 473 LYS cc_start: 0.8073 (mttp) cc_final: 0.7327 (mtpp) REVERT: B 475 ASN cc_start: 0.7944 (t0) cc_final: 0.7574 (t0) REVERT: B 487 ILE cc_start: 0.8623 (pt) cc_final: 0.8407 (mt) REVERT: B 488 MET cc_start: 0.7147 (tpp) cc_final: 0.5816 (tpp) REVERT: B 492 LEU cc_start: 0.8669 (mt) cc_final: 0.7742 (mt) REVERT: B 499 LEU cc_start: 0.8340 (tp) cc_final: 0.8026 (tp) REVERT: B 526 SER cc_start: 0.8507 (m) cc_final: 0.8260 (p) REVERT: B 556 TYR cc_start: 0.8330 (p90) cc_final: 0.8104 (p90) REVERT: B 580 LYS cc_start: 0.8260 (mmmt) cc_final: 0.8056 (mmmm) REVERT: B 677 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7104 (ttp80) REVERT: B 681 LYS cc_start: 0.8404 (ptmm) cc_final: 0.7983 (ttpp) REVERT: B 682 GLU cc_start: 0.8220 (tp30) cc_final: 0.7805 (tp30) REVERT: B 687 ASP cc_start: 0.6966 (t0) cc_final: 0.6569 (t0) REVERT: B 724 ASP cc_start: 0.7245 (m-30) cc_final: 0.6968 (m-30) outliers start: 53 outliers final: 41 residues processed: 330 average time/residue: 0.2555 time to fit residues: 115.4424 Evaluate side-chains 333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 464 GLN A 728 HIS B 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.132935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114123 restraints weight = 20383.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.117911 restraints weight = 11493.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.120427 restraints weight = 7308.193| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.167 Angle : 0.647 17.021 14128 Z= 0.334 Chirality : 0.044 0.243 1716 Planarity : 0.004 0.052 1757 Dihedral : 5.989 83.825 1450 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.43 % Allowed : 21.10 % Favored : 73.46 % 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: -1.16 (0.23), residues: 1319 helix: 0.29 (0.18), residues: 819 sheet: -2.57 (0.89), residues: 34 loop : -2.56 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.019 0.002 HIS A 728 PHE 0.016 0.001 PHE A 385 TYR 0.031 0.002 TYR A 556 ARG 0.005 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 544) hydrogen bonds : angle 4.09317 ( 1593) covalent geometry : bond 0.00351 (10395) covalent geometry : angle 0.64749 (14128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7610 (mmt90) REVERT: A 37 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: A 93 SER cc_start: 0.8503 (t) cc_final: 0.8147 (p) REVERT: A 101 GLN cc_start: 0.7532 (mt0) cc_final: 0.7267 (mm-40) REVERT: A 114 GLN cc_start: 0.7952 (pt0) cc_final: 0.7697 (pt0) REVERT: A 122 PHE cc_start: 0.7264 (m-80) cc_final: 0.6787 (m-10) REVERT: A 123 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7956 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8583 (tp) cc_final: 0.8105 (tp) REVERT: A 199 ILE cc_start: 0.8237 (mt) cc_final: 0.7894 (mt) REVERT: A 213 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7375 (mtm-85) REVERT: A 231 VAL cc_start: 0.8801 (t) cc_final: 0.8118 (p) REVERT: A 234 SER cc_start: 0.8781 (m) cc_final: 0.8274 (t) REVERT: A 235 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7779 (mm-40) REVERT: A 237 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8164 (ttpp) REVERT: A 280 ILE cc_start: 0.8951 (mt) cc_final: 0.8713 (tp) REVERT: A 286 LYS cc_start: 0.9188 (tppt) cc_final: 0.8838 (mmmm) REVERT: A 371 TYR cc_start: 0.8179 (m-80) cc_final: 0.7852 (m-80) REVERT: A 383 GLN cc_start: 0.7532 (mt0) cc_final: 0.7280 (mt0) REVERT: A 384 GLU cc_start: 0.6756 (mm-30) cc_final: 0.5957 (mm-30) REVERT: A 395 SER cc_start: 0.8409 (m) cc_final: 0.8045 (p) REVERT: A 398 PHE cc_start: 0.7065 (m-80) cc_final: 0.6516 (m-80) REVERT: A 447 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7913 (mttp) REVERT: A 457 ASN cc_start: 0.8165 (m110) cc_final: 0.7666 (m110) REVERT: A 464 GLN cc_start: 0.8710 (mt0) cc_final: 0.8434 (mt0) REVERT: A 473 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8068 (mtpt) REVERT: A 476 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8503 (mtpp) REVERT: A 484 PHE cc_start: 0.8275 (t80) cc_final: 0.7948 (t80) REVERT: A 488 MET cc_start: 0.7628 (tpp) cc_final: 0.7146 (tpp) REVERT: A 512 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: A 530 TYR cc_start: 0.7511 (m-80) cc_final: 0.7186 (m-80) REVERT: A 546 LYS cc_start: 0.8246 (tptm) cc_final: 0.7697 (tptm) REVERT: A 662 CYS cc_start: 0.7856 (m) cc_final: 0.7626 (m) REVERT: A 667 PHE cc_start: 0.7846 (p90) cc_final: 0.7493 (p90) REVERT: A 686 ILE cc_start: 0.8801 (pt) cc_final: 0.7803 (mm) REVERT: A 694 LEU cc_start: 0.8399 (mm) cc_final: 0.8196 (mm) REVERT: A 705 GLN cc_start: 0.8038 (pt0) cc_final: 0.7819 (tt0) REVERT: A 710 ASP cc_start: 0.7405 (p0) cc_final: 0.7083 (p0) REVERT: A 715 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7127 (mmmm) REVERT: A 716 ASP cc_start: 0.7284 (t0) cc_final: 0.6962 (t0) REVERT: B 38 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7850 (tpp80) REVERT: B 68 LEU cc_start: 0.8413 (mm) cc_final: 0.8080 (mt) REVERT: B 134 ARG cc_start: 0.6505 (mtt90) cc_final: 0.6288 (mtt90) REVERT: B 158 ASP cc_start: 0.5392 (m-30) cc_final: 0.4036 (m-30) REVERT: B 185 ARG cc_start: 0.7234 (mmt180) cc_final: 0.6130 (mmt180) REVERT: B 207 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 230 GLN cc_start: 0.7897 (tp40) cc_final: 0.7381 (tm-30) REVERT: B 231 VAL cc_start: 0.8703 (p) cc_final: 0.8014 (p) REVERT: B 235 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 236 LEU cc_start: 0.8086 (tp) cc_final: 0.7694 (tp) REVERT: B 237 LYS cc_start: 0.8253 (pttt) cc_final: 0.7847 (pttt) REVERT: B 251 LEU cc_start: 0.8495 (mm) cc_final: 0.6567 (mm) REVERT: B 255 TYR cc_start: 0.8220 (m-10) cc_final: 0.7698 (m-80) REVERT: B 259 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 263 ASN cc_start: 0.7440 (t0) cc_final: 0.6801 (t0) REVERT: B 271 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7455 (p0) REVERT: B 286 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7877 (tppp) REVERT: B 293 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7890 (mmtm) REVERT: B 320 GLU cc_start: 0.7630 (tp30) cc_final: 0.7406 (tp30) REVERT: B 324 ASN cc_start: 0.7742 (t0) cc_final: 0.7447 (t0) REVERT: B 340 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6809 (pp) REVERT: B 395 SER cc_start: 0.7879 (m) cc_final: 0.7306 (p) REVERT: B 457 ASN cc_start: 0.7230 (m110) cc_final: 0.6902 (m-40) REVERT: B 473 LYS cc_start: 0.8036 (mttp) cc_final: 0.7181 (mtpp) REVERT: B 475 ASN cc_start: 0.7978 (t0) cc_final: 0.7612 (t0) REVERT: B 487 ILE cc_start: 0.8620 (pt) cc_final: 0.8374 (mm) REVERT: B 488 MET cc_start: 0.7205 (tpp) cc_final: 0.5883 (tpp) REVERT: B 492 LEU cc_start: 0.8706 (mt) cc_final: 0.7764 (mt) REVERT: B 499 LEU cc_start: 0.8204 (tp) cc_final: 0.7917 (tp) REVERT: B 526 SER cc_start: 0.8542 (m) cc_final: 0.8306 (p) REVERT: B 556 TYR cc_start: 0.8311 (p90) cc_final: 0.8084 (p90) REVERT: B 580 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8039 (mmmm) REVERT: B 677 ARG cc_start: 0.7424 (ttt180) cc_final: 0.7081 (ttp80) REVERT: B 681 LYS cc_start: 0.8438 (ptmm) cc_final: 0.7961 (ttpp) REVERT: B 682 GLU cc_start: 0.8214 (tp30) cc_final: 0.7685 (tp30) REVERT: B 685 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7503 (ptp90) REVERT: B 687 ASP cc_start: 0.6972 (t0) cc_final: 0.6584 (t0) REVERT: B 724 ASP cc_start: 0.7315 (m-30) cc_final: 0.7042 (m-30) outliers start: 61 outliers final: 43 residues processed: 336 average time/residue: 0.2507 time to fit residues: 115.6512 Evaluate side-chains 339 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.132762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113775 restraints weight = 20564.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.117602 restraints weight = 11623.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120121 restraints weight = 7353.780| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10395 Z= 0.164 Angle : 0.657 13.599 14128 Z= 0.338 Chirality : 0.045 0.359 1716 Planarity : 0.004 0.053 1757 Dihedral : 5.915 87.863 1446 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.08 % Allowed : 21.46 % Favored : 73.46 % 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: -1.16 (0.23), residues: 1319 helix: 0.27 (0.18), residues: 824 sheet: -2.67 (0.88), residues: 34 loop : -2.52 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.013 0.001 HIS A 728 PHE 0.018 0.001 PHE A 385 TYR 0.027 0.002 TYR A 556 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 544) hydrogen bonds : angle 4.12461 ( 1593) covalent geometry : bond 0.00348 (10395) covalent geometry : angle 0.65702 (14128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7593 (mmt90) REVERT: A 37 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: A 93 SER cc_start: 0.8509 (t) cc_final: 0.8166 (p) REVERT: A 122 PHE cc_start: 0.7227 (m-80) cc_final: 0.6812 (m-10) REVERT: A 123 PRO cc_start: 0.8245 (Cg_exo) cc_final: 0.8010 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8598 (tp) cc_final: 0.8118 (tp) REVERT: A 199 ILE cc_start: 0.8224 (mt) cc_final: 0.7878 (mt) REVERT: A 231 VAL cc_start: 0.8752 (t) cc_final: 0.8045 (p) REVERT: A 234 SER cc_start: 0.8795 (m) cc_final: 0.8244 (t) REVERT: A 235 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7701 (mm-40) REVERT: A 237 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8152 (ttpp) REVERT: A 276 LEU cc_start: 0.8496 (mm) cc_final: 0.8229 (mm) REVERT: A 280 ILE cc_start: 0.8916 (mt) cc_final: 0.8691 (tp) REVERT: A 286 LYS cc_start: 0.9189 (tppt) cc_final: 0.8849 (mmmm) REVERT: A 371 TYR cc_start: 0.8140 (m-80) cc_final: 0.7799 (m-80) REVERT: A 383 GLN cc_start: 0.7244 (mt0) cc_final: 0.6547 (mp10) REVERT: A 384 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5919 (mm-30) REVERT: A 395 SER cc_start: 0.8458 (m) cc_final: 0.8104 (p) REVERT: A 447 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7858 (mttp) REVERT: A 457 ASN cc_start: 0.8137 (m110) cc_final: 0.7635 (m110) REVERT: A 473 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7950 (mtpt) REVERT: A 484 PHE cc_start: 0.8214 (t80) cc_final: 0.7908 (t80) REVERT: A 488 MET cc_start: 0.7536 (tpp) cc_final: 0.7021 (tpp) REVERT: A 511 LEU cc_start: 0.8832 (mt) cc_final: 0.8621 (mm) REVERT: A 530 TYR cc_start: 0.7500 (m-80) cc_final: 0.7239 (m-80) REVERT: A 546 LYS cc_start: 0.8219 (tptm) cc_final: 0.7699 (tptm) REVERT: A 549 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.7092 (ttm-80) REVERT: A 566 ILE cc_start: 0.8713 (mm) cc_final: 0.8498 (mt) REVERT: A 662 CYS cc_start: 0.7810 (m) cc_final: 0.7542 (m) REVERT: A 667 PHE cc_start: 0.7780 (p90) cc_final: 0.7459 (p90) REVERT: A 686 ILE cc_start: 0.8401 (pt) cc_final: 0.8182 (mm) REVERT: A 694 LEU cc_start: 0.8426 (mm) cc_final: 0.8186 (mm) REVERT: A 705 GLN cc_start: 0.8011 (pt0) cc_final: 0.7789 (tt0) REVERT: A 715 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7129 (mmmm) REVERT: A 716 ASP cc_start: 0.7255 (t0) cc_final: 0.6916 (t0) REVERT: A 723 HIS cc_start: 0.7214 (t-90) cc_final: 0.6971 (t-90) REVERT: B 68 LEU cc_start: 0.8432 (mm) cc_final: 0.8069 (mt) REVERT: B 134 ARG cc_start: 0.6511 (mtt90) cc_final: 0.6299 (mtt90) REVERT: B 207 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 230 GLN cc_start: 0.7853 (tp40) cc_final: 0.7343 (tm-30) REVERT: B 231 VAL cc_start: 0.8683 (p) cc_final: 0.7955 (p) REVERT: B 235 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7281 (mm-40) REVERT: B 236 LEU cc_start: 0.8054 (tp) cc_final: 0.7644 (tp) REVERT: B 237 LYS cc_start: 0.8209 (pttt) cc_final: 0.7803 (pttt) REVERT: B 251 LEU cc_start: 0.8463 (mm) cc_final: 0.6559 (mm) REVERT: B 255 TYR cc_start: 0.8144 (m-10) cc_final: 0.7685 (m-80) REVERT: B 259 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7976 (tm-30) REVERT: B 263 ASN cc_start: 0.7208 (t0) cc_final: 0.6664 (t0) REVERT: B 271 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 286 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7825 (tppp) REVERT: B 293 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8027 (mmtm) REVERT: B 320 GLU cc_start: 0.7553 (tp30) cc_final: 0.7314 (tp30) REVERT: B 324 ASN cc_start: 0.7832 (t0) cc_final: 0.7539 (t0) REVERT: B 340 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6906 (pp) REVERT: B 395 SER cc_start: 0.8051 (m) cc_final: 0.7519 (p) REVERT: B 457 ASN cc_start: 0.7257 (m110) cc_final: 0.6974 (m-40) REVERT: B 473 LYS cc_start: 0.8059 (mttp) cc_final: 0.7166 (mtpp) REVERT: B 475 ASN cc_start: 0.7987 (t0) cc_final: 0.7691 (t0) REVERT: B 487 ILE cc_start: 0.8617 (pt) cc_final: 0.8405 (mt) REVERT: B 488 MET cc_start: 0.6995 (tpp) cc_final: 0.5746 (tpp) REVERT: B 492 LEU cc_start: 0.8588 (mt) cc_final: 0.7349 (mt) REVERT: B 499 LEU cc_start: 0.8235 (tp) cc_final: 0.7944 (tp) REVERT: B 526 SER cc_start: 0.8561 (m) cc_final: 0.8336 (p) REVERT: B 556 TYR cc_start: 0.8211 (p90) cc_final: 0.8001 (p90) REVERT: B 580 LYS cc_start: 0.8260 (mmmt) cc_final: 0.8043 (mmmm) REVERT: B 677 ARG cc_start: 0.7385 (ttt180) cc_final: 0.7076 (ttp80) REVERT: B 681 LYS cc_start: 0.8432 (ptmm) cc_final: 0.8013 (ttpp) REVERT: B 682 GLU cc_start: 0.8185 (tp30) cc_final: 0.7851 (tp30) REVERT: B 687 ASP cc_start: 0.6917 (t0) cc_final: 0.6523 (t0) REVERT: B 724 ASP cc_start: 0.7355 (m-30) cc_final: 0.7087 (m-30) outliers start: 57 outliers final: 48 residues processed: 329 average time/residue: 0.2528 time to fit residues: 115.1201 Evaluate side-chains 342 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.112187 restraints weight = 20473.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116003 restraints weight = 11682.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118523 restraints weight = 7419.606| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.190 Angle : 0.690 12.485 14128 Z= 0.357 Chirality : 0.045 0.320 1716 Planarity : 0.005 0.056 1757 Dihedral : 5.563 53.333 1443 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 5.25 % Allowed : 21.99 % Favored : 72.75 % 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: -1.12 (0.23), residues: 1319 helix: 0.29 (0.18), residues: 819 sheet: -2.68 (0.89), residues: 34 loop : -2.46 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 83 HIS 0.012 0.001 HIS A 728 PHE 0.025 0.001 PHE B 484 TYR 0.027 0.002 TYR A 556 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 544) hydrogen bonds : angle 4.23485 ( 1593) covalent geometry : bond 0.00398 (10395) covalent geometry : angle 0.69020 (14128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7681 (mmt90) REVERT: A 37 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: A 93 SER cc_start: 0.8511 (t) cc_final: 0.8184 (p) REVERT: A 122 PHE cc_start: 0.7231 (m-80) cc_final: 0.6806 (m-10) REVERT: A 123 PRO cc_start: 0.8238 (Cg_exo) cc_final: 0.7998 (Cg_endo) REVERT: A 145 SER cc_start: 0.8135 (m) cc_final: 0.7736 (p) REVERT: A 195 LEU cc_start: 0.8662 (tp) cc_final: 0.8197 (tp) REVERT: A 199 ILE cc_start: 0.8232 (mt) cc_final: 0.7891 (mt) REVERT: A 213 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7453 (mtm-85) REVERT: A 231 VAL cc_start: 0.8741 (t) cc_final: 0.8048 (p) REVERT: A 234 SER cc_start: 0.8804 (m) cc_final: 0.8181 (t) REVERT: A 235 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7716 (mm-40) REVERT: A 237 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8225 (ttpp) REVERT: A 276 LEU cc_start: 0.8503 (mm) cc_final: 0.8111 (mm) REVERT: A 279 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 286 LYS cc_start: 0.9192 (tppt) cc_final: 0.8854 (mmmm) REVERT: A 320 GLU cc_start: 0.6718 (tp30) cc_final: 0.6334 (tp30) REVERT: A 371 TYR cc_start: 0.8178 (m-80) cc_final: 0.7848 (m-80) REVERT: A 383 GLN cc_start: 0.7225 (mt0) cc_final: 0.6711 (mp10) REVERT: A 384 GLU cc_start: 0.6625 (mm-30) cc_final: 0.5887 (mm-30) REVERT: A 395 SER cc_start: 0.8446 (m) cc_final: 0.8093 (p) REVERT: A 447 LYS cc_start: 0.8382 (mtpt) cc_final: 0.7881 (mttp) REVERT: A 457 ASN cc_start: 0.8184 (m110) cc_final: 0.7785 (m-40) REVERT: A 473 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7958 (mtpt) REVERT: A 484 PHE cc_start: 0.8229 (t80) cc_final: 0.7928 (t80) REVERT: A 488 MET cc_start: 0.7586 (tpp) cc_final: 0.7039 (tpp) REVERT: A 530 TYR cc_start: 0.7578 (m-80) cc_final: 0.7349 (m-80) REVERT: A 537 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7635 (mttm) REVERT: A 546 LYS cc_start: 0.8229 (tptm) cc_final: 0.7677 (tptm) REVERT: A 549 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.7044 (ttm-80) REVERT: A 662 CYS cc_start: 0.7823 (m) cc_final: 0.7560 (m) REVERT: A 667 PHE cc_start: 0.7772 (p90) cc_final: 0.7466 (p90) REVERT: A 684 GLN cc_start: 0.7508 (tp40) cc_final: 0.7305 (tp-100) REVERT: A 686 ILE cc_start: 0.8449 (pt) cc_final: 0.8197 (mm) REVERT: A 694 LEU cc_start: 0.8478 (mm) cc_final: 0.8257 (mm) REVERT: A 705 GLN cc_start: 0.7996 (pt0) cc_final: 0.7784 (tt0) REVERT: A 715 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7214 (mmmm) REVERT: A 716 ASP cc_start: 0.7334 (t0) cc_final: 0.6891 (t0) REVERT: A 724 ASP cc_start: 0.6782 (m-30) cc_final: 0.6312 (m-30) REVERT: B 68 LEU cc_start: 0.8423 (mm) cc_final: 0.8064 (mt) REVERT: B 134 ARG cc_start: 0.6507 (mtt90) cc_final: 0.6307 (mtt90) REVERT: B 185 ARG cc_start: 0.7420 (mmt180) cc_final: 0.6549 (mmt180) REVERT: B 207 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 230 GLN cc_start: 0.7862 (tp40) cc_final: 0.7317 (tm-30) REVERT: B 231 VAL cc_start: 0.8667 (p) cc_final: 0.7938 (p) REVERT: B 235 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7277 (mm-40) REVERT: B 236 LEU cc_start: 0.8044 (tp) cc_final: 0.7642 (tp) REVERT: B 237 LYS cc_start: 0.8238 (pttt) cc_final: 0.7846 (pttt) REVERT: B 251 LEU cc_start: 0.8466 (mm) cc_final: 0.6552 (mm) REVERT: B 255 TYR cc_start: 0.8136 (m-10) cc_final: 0.7717 (m-80) REVERT: B 259 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 263 ASN cc_start: 0.7246 (t0) cc_final: 0.6684 (t0) REVERT: B 271 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 286 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7843 (tppp) REVERT: B 293 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8113 (mmtm) REVERT: B 320 GLU cc_start: 0.7635 (tp30) cc_final: 0.7361 (tp30) REVERT: B 324 ASN cc_start: 0.7961 (t0) cc_final: 0.7697 (t0) REVERT: B 340 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6927 (pp) REVERT: B 395 SER cc_start: 0.8098 (m) cc_final: 0.7571 (p) REVERT: B 457 ASN cc_start: 0.7327 (m110) cc_final: 0.7036 (m-40) REVERT: B 473 LYS cc_start: 0.8042 (mttp) cc_final: 0.7294 (ttpp) REVERT: B 475 ASN cc_start: 0.7962 (t0) cc_final: 0.7676 (t0) REVERT: B 487 ILE cc_start: 0.8638 (pt) cc_final: 0.8405 (mt) REVERT: B 488 MET cc_start: 0.7040 (tpp) cc_final: 0.5754 (tpp) REVERT: B 492 LEU cc_start: 0.8666 (mt) cc_final: 0.7307 (mt) REVERT: B 499 LEU cc_start: 0.8276 (tp) cc_final: 0.7983 (tp) REVERT: B 580 LYS cc_start: 0.8281 (mmmt) cc_final: 0.8064 (mmmm) REVERT: B 677 ARG cc_start: 0.7370 (ttt180) cc_final: 0.7085 (ttp80) REVERT: B 681 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8040 (ttpp) REVERT: B 682 GLU cc_start: 0.8190 (tp30) cc_final: 0.7873 (tp30) REVERT: B 687 ASP cc_start: 0.6941 (t0) cc_final: 0.6548 (t0) REVERT: B 724 ASP cc_start: 0.7263 (m-30) cc_final: 0.7039 (m-30) outliers start: 59 outliers final: 48 residues processed: 333 average time/residue: 0.2559 time to fit residues: 119.5106 Evaluate side-chains 344 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 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 207 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111529 restraints weight = 20611.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115430 restraints weight = 11502.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118012 restraints weight = 7262.282| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10395 Z= 0.177 Angle : 0.701 11.505 14128 Z= 0.360 Chirality : 0.046 0.310 1716 Planarity : 0.005 0.071 1757 Dihedral : 5.593 53.288 1443 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 5.25 % Allowed : 22.80 % Favored : 71.95 % 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: -1.09 (0.23), residues: 1319 helix: 0.33 (0.18), residues: 812 sheet: -2.82 (0.98), residues: 28 loop : -2.43 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 83 HIS 0.014 0.001 HIS A 728 PHE 0.029 0.001 PHE A 210 TYR 0.027 0.002 TYR A 691 ARG 0.005 0.001 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 544) hydrogen bonds : angle 4.19134 ( 1593) covalent geometry : bond 0.00380 (10395) covalent geometry : angle 0.70063 (14128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 297 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7778 (mmt90) REVERT: A 37 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 79 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7638 (mmt90) REVERT: A 93 SER cc_start: 0.8630 (t) cc_final: 0.8269 (p) REVERT: A 113 VAL cc_start: 0.8128 (t) cc_final: 0.7860 (p) REVERT: A 122 PHE cc_start: 0.7175 (m-80) cc_final: 0.6703 (m-10) REVERT: A 123 PRO cc_start: 0.8172 (Cg_exo) cc_final: 0.7889 (Cg_endo) REVERT: A 142 PRO cc_start: 0.8075 (Cg_endo) cc_final: 0.7865 (Cg_exo) REVERT: A 145 SER cc_start: 0.8195 (m) cc_final: 0.7797 (p) REVERT: A 195 LEU cc_start: 0.8582 (tp) cc_final: 0.8122 (tp) REVERT: A 199 ILE cc_start: 0.8205 (mt) cc_final: 0.7863 (mt) REVERT: A 213 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7437 (mtm-85) REVERT: A 217 ASP cc_start: 0.7909 (m-30) cc_final: 0.7055 (m-30) REVERT: A 231 VAL cc_start: 0.8791 (t) cc_final: 0.8101 (p) REVERT: A 234 SER cc_start: 0.8733 (m) cc_final: 0.8224 (t) REVERT: A 235 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7798 (mm-40) REVERT: A 237 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8235 (ttpp) REVERT: A 276 LEU cc_start: 0.8610 (mm) cc_final: 0.8250 (mm) REVERT: A 279 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 280 ILE cc_start: 0.8966 (mt) cc_final: 0.8739 (tp) REVERT: A 283 MET cc_start: 0.7979 (tpp) cc_final: 0.7549 (mpp) REVERT: A 286 LYS cc_start: 0.9189 (tppt) cc_final: 0.8877 (mmmm) REVERT: A 371 TYR cc_start: 0.8154 (m-80) cc_final: 0.7814 (m-80) REVERT: A 383 GLN cc_start: 0.7327 (mt0) cc_final: 0.7001 (mp10) REVERT: A 385 PHE cc_start: 0.8371 (t80) cc_final: 0.8165 (t80) REVERT: A 395 SER cc_start: 0.8437 (m) cc_final: 0.8074 (p) REVERT: A 438 LEU cc_start: 0.8002 (tp) cc_final: 0.7756 (tp) REVERT: A 447 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7934 (mttp) REVERT: A 457 ASN cc_start: 0.8301 (m110) cc_final: 0.7804 (m-40) REVERT: A 459 LYS cc_start: 0.8752 (tppp) cc_final: 0.8322 (tppp) REVERT: A 467 ASP cc_start: 0.7630 (m-30) cc_final: 0.7370 (p0) REVERT: A 473 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8050 (mtpt) REVERT: A 484 PHE cc_start: 0.8295 (t80) cc_final: 0.7921 (t80) REVERT: A 488 MET cc_start: 0.7743 (tpp) cc_final: 0.7120 (tpp) REVERT: A 530 TYR cc_start: 0.7625 (m-80) cc_final: 0.7389 (m-80) REVERT: A 537 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7629 (mttp) REVERT: A 546 LYS cc_start: 0.8261 (tptm) cc_final: 0.7631 (tptm) REVERT: A 549 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.7090 (ttm-80) REVERT: A 662 CYS cc_start: 0.7887 (m) cc_final: 0.7586 (m) REVERT: A 667 PHE cc_start: 0.7889 (p90) cc_final: 0.7569 (p90) REVERT: A 684 GLN cc_start: 0.7627 (tp40) cc_final: 0.7410 (tp40) REVERT: A 686 ILE cc_start: 0.8474 (pt) cc_final: 0.8243 (mm) REVERT: A 694 LEU cc_start: 0.8427 (mm) cc_final: 0.8165 (mm) REVERT: A 715 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7151 (mmmm) REVERT: A 716 ASP cc_start: 0.7390 (t0) cc_final: 0.6912 (t0) REVERT: A 723 HIS cc_start: 0.7352 (t70) cc_final: 0.7066 (t-90) REVERT: A 724 ASP cc_start: 0.6922 (m-30) cc_final: 0.6434 (m-30) REVERT: A 730 GLN cc_start: 0.8544 (mt0) cc_final: 0.7983 (mp10) REVERT: B 68 LEU cc_start: 0.8420 (mm) cc_final: 0.8058 (mt) REVERT: B 207 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 230 GLN cc_start: 0.7982 (tp40) cc_final: 0.7419 (tm-30) REVERT: B 231 VAL cc_start: 0.8643 (p) cc_final: 0.7916 (p) REVERT: B 235 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7347 (mm-40) REVERT: B 236 LEU cc_start: 0.7998 (tp) cc_final: 0.7649 (tp) REVERT: B 237 LYS cc_start: 0.8353 (pttt) cc_final: 0.7906 (pttt) REVERT: B 251 LEU cc_start: 0.8465 (mm) cc_final: 0.6631 (mm) REVERT: B 255 TYR cc_start: 0.8259 (m-10) cc_final: 0.7735 (m-80) REVERT: B 259 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 263 ASN cc_start: 0.7474 (t0) cc_final: 0.6833 (t0) REVERT: B 271 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7713 (p0) REVERT: B 293 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8217 (mmtm) REVERT: B 320 GLU cc_start: 0.7884 (tp30) cc_final: 0.7592 (tp30) REVERT: B 324 ASN cc_start: 0.8137 (t0) cc_final: 0.7858 (t0) REVERT: B 340 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6883 (pp) REVERT: B 395 SER cc_start: 0.8030 (m) cc_final: 0.7477 (p) REVERT: B 457 ASN cc_start: 0.7464 (m110) cc_final: 0.7150 (m-40) REVERT: B 473 LYS cc_start: 0.8073 (mttp) cc_final: 0.7242 (ttpp) REVERT: B 475 ASN cc_start: 0.7950 (t0) cc_final: 0.7017 (m-40) REVERT: B 488 MET cc_start: 0.7174 (tpp) cc_final: 0.5882 (tpp) REVERT: B 492 LEU cc_start: 0.8733 (mt) cc_final: 0.7388 (mt) REVERT: B 499 LEU cc_start: 0.8232 (tp) cc_final: 0.7952 (tp) REVERT: B 580 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8089 (mmmm) REVERT: B 677 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7232 (ttp80) REVERT: B 681 LYS cc_start: 0.8458 (ptmm) cc_final: 0.8047 (ttpp) REVERT: B 682 GLU cc_start: 0.8221 (tp30) cc_final: 0.7872 (tp30) REVERT: B 687 ASP cc_start: 0.7078 (t0) cc_final: 0.6662 (t0) REVERT: B 720 LEU cc_start: 0.8406 (mp) cc_final: 0.8170 (mp) REVERT: B 724 ASP cc_start: 0.7328 (m-30) cc_final: 0.7100 (m-30) outliers start: 59 outliers final: 48 residues processed: 333 average time/residue: 0.2355 time to fit residues: 108.8064 Evaluate side-chains 357 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110959 restraints weight = 20749.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.114887 restraints weight = 11644.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117524 restraints weight = 7357.026| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10395 Z= 0.178 Angle : 0.727 11.742 14128 Z= 0.370 Chirality : 0.047 0.406 1716 Planarity : 0.005 0.070 1757 Dihedral : 5.592 53.332 1441 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 4.81 % Allowed : 22.89 % Favored : 72.31 % 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: -1.13 (0.23), residues: 1319 helix: 0.28 (0.18), residues: 819 sheet: -2.90 (0.98), residues: 28 loop : -2.47 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 83 HIS 0.015 0.001 HIS A 728 PHE 0.026 0.001 PHE A 130 TYR 0.028 0.002 TYR A 691 ARG 0.008 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 544) hydrogen bonds : angle 4.24342 ( 1593) covalent geometry : bond 0.00384 (10395) covalent geometry : angle 0.72665 (14128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7757 (mmt90) REVERT: A 37 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: A 79 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7661 (mmt90) REVERT: A 93 SER cc_start: 0.8622 (t) cc_final: 0.8262 (p) REVERT: A 113 VAL cc_start: 0.8049 (t) cc_final: 0.7835 (p) REVERT: A 122 PHE cc_start: 0.7160 (m-80) cc_final: 0.6702 (m-10) REVERT: A 123 PRO cc_start: 0.8168 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: A 145 SER cc_start: 0.8189 (m) cc_final: 0.7784 (p) REVERT: A 195 LEU cc_start: 0.8607 (tp) cc_final: 0.8140 (tp) REVERT: A 199 ILE cc_start: 0.8219 (mt) cc_final: 0.7874 (mt) REVERT: A 213 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7404 (mtm-85) REVERT: A 217 ASP cc_start: 0.7891 (m-30) cc_final: 0.7098 (m-30) REVERT: A 231 VAL cc_start: 0.8781 (t) cc_final: 0.8108 (p) REVERT: A 234 SER cc_start: 0.8736 (m) cc_final: 0.8230 (t) REVERT: A 235 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7815 (mm-40) REVERT: A 237 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8224 (ttpp) REVERT: A 241 ASN cc_start: 0.8324 (t0) cc_final: 0.8025 (t0) REVERT: A 276 LEU cc_start: 0.8595 (mm) cc_final: 0.8239 (mm) REVERT: A 279 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 280 ILE cc_start: 0.8940 (mt) cc_final: 0.8728 (tp) REVERT: A 283 MET cc_start: 0.7965 (tpp) cc_final: 0.7528 (mpp) REVERT: A 286 LYS cc_start: 0.9186 (tppt) cc_final: 0.8874 (mmmm) REVERT: A 320 GLU cc_start: 0.6855 (tp30) cc_final: 0.6391 (tp30) REVERT: A 371 TYR cc_start: 0.8164 (m-80) cc_final: 0.7882 (m-80) REVERT: A 383 GLN cc_start: 0.7435 (mt0) cc_final: 0.6820 (mp10) REVERT: A 384 GLU cc_start: 0.6721 (mm-30) cc_final: 0.5945 (mm-30) REVERT: A 395 SER cc_start: 0.8418 (m) cc_final: 0.8030 (p) REVERT: A 438 LEU cc_start: 0.8001 (tp) cc_final: 0.7751 (tp) REVERT: A 447 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7912 (mttp) REVERT: A 457 ASN cc_start: 0.8306 (m110) cc_final: 0.7841 (m110) REVERT: A 459 LYS cc_start: 0.8752 (tppp) cc_final: 0.8327 (tppp) REVERT: A 467 ASP cc_start: 0.7629 (m-30) cc_final: 0.7378 (p0) REVERT: A 473 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8065 (mtpt) REVERT: A 484 PHE cc_start: 0.8283 (t80) cc_final: 0.7866 (t80) REVERT: A 488 MET cc_start: 0.7707 (tpp) cc_final: 0.7079 (tpp) REVERT: A 530 TYR cc_start: 0.7670 (m-80) cc_final: 0.7376 (m-80) REVERT: A 537 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7585 (mttm) REVERT: A 546 LYS cc_start: 0.8292 (tptm) cc_final: 0.7670 (tptm) REVERT: A 568 SER cc_start: 0.8908 (m) cc_final: 0.8685 (p) REVERT: A 662 CYS cc_start: 0.7845 (m) cc_final: 0.7595 (m) REVERT: A 667 PHE cc_start: 0.7847 (p90) cc_final: 0.7547 (p90) REVERT: A 686 ILE cc_start: 0.8512 (pt) cc_final: 0.8284 (mm) REVERT: A 694 LEU cc_start: 0.8440 (mm) cc_final: 0.8213 (mm) REVERT: A 715 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7179 (mmmm) REVERT: A 716 ASP cc_start: 0.7414 (t0) cc_final: 0.6940 (t0) REVERT: A 723 HIS cc_start: 0.7352 (t70) cc_final: 0.7043 (t-90) REVERT: A 724 ASP cc_start: 0.6896 (m-30) cc_final: 0.6398 (m-30) REVERT: B 68 LEU cc_start: 0.8457 (mm) cc_final: 0.8099 (mt) REVERT: B 134 ARG cc_start: 0.6443 (mtt90) cc_final: 0.6088 (mtt90) REVERT: B 207 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 230 GLN cc_start: 0.7973 (tp40) cc_final: 0.7390 (tm-30) REVERT: B 231 VAL cc_start: 0.8651 (p) cc_final: 0.7924 (p) REVERT: B 235 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7280 (mm-40) REVERT: B 236 LEU cc_start: 0.7985 (tp) cc_final: 0.7432 (tp) REVERT: B 237 LYS cc_start: 0.8383 (pttt) cc_final: 0.7941 (pttt) REVERT: B 251 LEU cc_start: 0.8443 (mm) cc_final: 0.6587 (mm) REVERT: B 255 TYR cc_start: 0.8249 (m-10) cc_final: 0.7708 (m-80) REVERT: B 259 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 263 ASN cc_start: 0.7328 (t0) cc_final: 0.6727 (t0) REVERT: B 271 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 293 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8373 (mmmm) REVERT: B 320 GLU cc_start: 0.7872 (tp30) cc_final: 0.7612 (tp30) REVERT: B 324 ASN cc_start: 0.8130 (t0) cc_final: 0.7863 (t0) REVERT: B 340 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6869 (pp) REVERT: B 395 SER cc_start: 0.8029 (m) cc_final: 0.7454 (p) REVERT: B 457 ASN cc_start: 0.7508 (m110) cc_final: 0.7159 (m-40) REVERT: B 462 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7870 (t80) REVERT: B 473 LYS cc_start: 0.8118 (mttp) cc_final: 0.7588 (ttpp) REVERT: B 488 MET cc_start: 0.7174 (tpp) cc_final: 0.5670 (tpp) REVERT: B 492 LEU cc_start: 0.8729 (mt) cc_final: 0.7275 (mt) REVERT: B 499 LEU cc_start: 0.8197 (tp) cc_final: 0.7941 (tt) REVERT: B 503 LEU cc_start: 0.8150 (mm) cc_final: 0.7883 (mp) REVERT: B 556 TYR cc_start: 0.8341 (p90) cc_final: 0.8128 (p90) REVERT: B 580 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8085 (mmmm) REVERT: B 677 ARG cc_start: 0.7518 (ttt180) cc_final: 0.7269 (ttp80) REVERT: B 681 LYS cc_start: 0.8474 (ptmm) cc_final: 0.8074 (ttpp) REVERT: B 682 GLU cc_start: 0.8226 (tp30) cc_final: 0.7889 (tp30) REVERT: B 687 ASP cc_start: 0.7085 (t0) cc_final: 0.6673 (t0) REVERT: B 724 ASP cc_start: 0.7417 (m-30) cc_final: 0.7196 (m-30) outliers start: 54 outliers final: 45 residues processed: 329 average time/residue: 0.2279 time to fit residues: 103.6681 Evaluate side-chains 339 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.111101 restraints weight = 20547.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.114984 restraints weight = 11546.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117629 restraints weight = 7310.013| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10395 Z= 0.174 Angle : 0.728 10.569 14128 Z= 0.373 Chirality : 0.046 0.372 1716 Planarity : 0.005 0.068 1757 Dihedral : 5.616 53.149 1441 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 4.36 % Allowed : 24.40 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1319 helix: 0.31 (0.18), residues: 813 sheet: -2.92 (0.98), residues: 28 loop : -2.44 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 83 HIS 0.016 0.001 HIS A 728 PHE 0.025 0.001 PHE A 130 TYR 0.026 0.002 TYR A 691 ARG 0.014 0.001 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 544) hydrogen bonds : angle 4.23917 ( 1593) covalent geometry : bond 0.00379 (10395) covalent geometry : angle 0.72817 (14128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.97 seconds wall clock time: 72 minutes 9.82 seconds (4329.82 seconds total)