Starting phenix.real_space_refine on Fri Feb 14 13:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wla_32579/02_2025/7wla_32579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wla_32579/02_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_32579/02_2025/7wla_32579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wla_32579/02_2025/7wla_32579.map" model { file = "/net/cci-nas-00/data/ceres_data/7wla_32579/02_2025/7wla_32579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wla_32579/02_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-5592/modules/chem_data/mon_lib" Total number of atoms: 10193 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.93, per 1000 atoms: 0.58 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: 2.44 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: 1.10 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: 2.86 Time building geometry restraints manager: 2.85 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: 2.650 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.220 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- 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= 0.108 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 *********************** 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 : 1.107 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: 0.2687 time to fit residues: 147.4678 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 : 1.077 ------------------------------------------------------------------------------- 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 = 0.138442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.119278 restraints weight = 20352.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123189 restraints weight = 11391.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.125791 restraints weight = 7229.227| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10395 Z= 0.257 Angle : 0.629 7.242 14128 Z= 0.330 Chirality : 0.043 0.212 1716 Planarity : 0.005 0.047 1757 Dihedral : 5.846 80.241 1458 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.81 % Allowed : 14.16 % 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: -0.63 (0.17), residues: 812 sheet: -2.95 (0.80), residues: 32 loop : -2.96 (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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7654 (tpp-160) cc_final: 0.7312 (mmt90) REVERT: A 93 SER cc_start: 0.8515 (t) cc_final: 0.8106 (p) REVERT: A 122 PHE cc_start: 0.7320 (m-80) cc_final: 0.6842 (m-10) REVERT: A 123 PRO cc_start: 0.8383 (Cg_exo) cc_final: 0.8153 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8523 (tp) cc_final: 0.7953 (tp) REVERT: A 199 ILE cc_start: 0.8204 (mt) cc_final: 0.7868 (mt) REVERT: A 231 VAL cc_start: 0.8733 (t) cc_final: 0.8001 (p) REVERT: A 235 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7676 (mm-40) REVERT: A 237 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8012 (ttpp) REVERT: A 247 TYR cc_start: 0.7426 (m-10) cc_final: 0.6310 (m-10) REVERT: A 272 PHE cc_start: 0.7955 (t80) cc_final: 0.7400 (t80) REVERT: A 280 ILE cc_start: 0.8958 (mt) cc_final: 0.8743 (tp) REVERT: A 286 LYS cc_start: 0.9168 (tppt) cc_final: 0.8784 (mmmm) REVERT: A 355 SER cc_start: 0.7884 (m) cc_final: 0.7560 (p) REVERT: A 384 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6033 (mm-30) REVERT: A 395 SER cc_start: 0.8612 (m) cc_final: 0.8094 (p) REVERT: A 398 PHE cc_start: 0.7158 (m-80) cc_final: 0.6406 (m-10) REVERT: A 432 MET cc_start: 0.7423 (tpt) cc_final: 0.6785 (tpt) REVERT: A 443 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6991 (pp20) REVERT: A 473 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7903 (mtpt) REVERT: A 484 PHE cc_start: 0.8326 (t80) cc_final: 0.7934 (t80) REVERT: A 488 MET cc_start: 0.7560 (tpp) cc_final: 0.7076 (tpp) REVERT: A 512 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: A 530 TYR cc_start: 0.7300 (m-80) cc_final: 0.7045 (m-80) REVERT: A 546 LYS cc_start: 0.8270 (tptm) cc_final: 0.7769 (tptm) REVERT: A 549 ARG cc_start: 0.6971 (ttt90) cc_final: 0.6238 (ttm-80) REVERT: A 556 TYR cc_start: 0.8154 (p90) cc_final: 0.7805 (p90) REVERT: A 560 ASP cc_start: 0.8191 (m-30) cc_final: 0.7936 (t0) REVERT: A 563 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7946 (ttmm) REVERT: A 662 CYS cc_start: 0.7951 (m) cc_final: 0.7481 (m) REVERT: A 686 ILE cc_start: 0.8631 (pt) cc_final: 0.8372 (mm) REVERT: A 687 ASP cc_start: 0.6844 (t0) cc_final: 0.6428 (t0) REVERT: A 723 HIS cc_start: 0.7123 (t-170) cc_final: 0.6888 (t-90) REVERT: B 29 GLU cc_start: 0.6812 (mp0) cc_final: 0.6570 (mp0) REVERT: B 118 TYR cc_start: 0.7142 (m-10) cc_final: 0.6783 (m-80) REVERT: B 195 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6251 (tp) REVERT: B 199 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 207 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 230 GLN cc_start: 0.7911 (tp40) cc_final: 0.7330 (tm-30) REVERT: B 231 VAL cc_start: 0.8663 (p) cc_final: 0.7892 (p) REVERT: B 235 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7260 (mm-40) REVERT: B 236 LEU cc_start: 0.8057 (tp) cc_final: 0.7690 (tp) REVERT: B 237 LYS cc_start: 0.8238 (pttt) cc_final: 0.7735 (pmtt) REVERT: B 251 LEU cc_start: 0.8424 (mm) cc_final: 0.6746 (mm) REVERT: B 255 TYR cc_start: 0.8239 (m-10) cc_final: 0.7700 (m-80) REVERT: B 259 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 263 ASN cc_start: 0.7381 (t0) cc_final: 0.6985 (t0) REVERT: B 271 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7636 (p0) REVERT: B 286 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7989 (ttmm) REVERT: B 293 LYS cc_start: 0.8573 (pptt) cc_final: 0.8259 (tppt) REVERT: B 309 ILE cc_start: 0.8865 (pt) cc_final: 0.8641 (mm) REVERT: B 320 GLU cc_start: 0.7640 (tp30) cc_final: 0.7303 (tp30) REVERT: B 359 VAL cc_start: 0.7878 (p) cc_final: 0.7538 (m) REVERT: B 395 SER cc_start: 0.7589 (m) cc_final: 0.7059 (p) REVERT: B 487 ILE cc_start: 0.8600 (pt) cc_final: 0.8123 (mm) REVERT: B 488 MET cc_start: 0.7192 (tpp) cc_final: 0.5998 (tpp) REVERT: B 492 LEU cc_start: 0.8553 (mt) cc_final: 0.7747 (mt) REVERT: B 499 LEU cc_start: 0.8283 (tp) cc_final: 0.8028 (tp) REVERT: B 560 ASP cc_start: 0.8017 (p0) cc_final: 0.7771 (p0) REVERT: B 583 LYS cc_start: 0.8800 (tmmt) cc_final: 0.8464 (tttm) REVERT: B 677 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7073 (ttp80) REVERT: B 682 GLU cc_start: 0.8010 (tp30) cc_final: 0.7751 (tp30) REVERT: B 701 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6959 (mm-30) REVERT: B 702 LYS cc_start: 0.7187 (tttm) cc_final: 0.6278 (tptp) REVERT: B 705 GLN cc_start: 0.8319 (tt0) cc_final: 0.8064 (tt0) REVERT: B 706 CYS cc_start: 0.7344 (m) cc_final: 0.5820 (m) outliers start: 54 outliers final: 33 residues processed: 350 average time/residue: 0.2659 time to fit residues: 126.3489 Evaluate side-chains 329 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 307 THR 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: 3.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115801 restraints weight = 20694.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119675 restraints weight = 11570.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122237 restraints weight = 7289.321| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3424 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= 0.237 Angle : 0.631 8.363 14128 Z= 0.331 Chirality : 0.043 0.199 1716 Planarity : 0.005 0.051 1757 Dihedral : 5.817 82.201 1450 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.72 % Allowed : 17.10 % Favored : 78.18 % 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: -1.74 (0.22), residues: 1319 helix: -0.19 (0.18), residues: 822 sheet: -2.44 (0.90), residues: 32 loop : -2.81 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.011 0.001 HIS A 728 PHE 0.024 0.001 PHE A 719 TYR 0.021 0.002 TYR A 556 ARG 0.007 0.001 ARG B 24 *********************** 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 358 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 1.059 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 34 GLN cc_start: 0.7681 (mm110) cc_final: 0.7396 (mm110) REVERT: A 36 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7279 (mmt90) REVERT: A 37 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 79 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7494 (mmt90) REVERT: A 93 SER cc_start: 0.8477 (t) cc_final: 0.8126 (p) REVERT: A 122 PHE cc_start: 0.7313 (m-80) cc_final: 0.6817 (m-10) REVERT: A 123 PRO cc_start: 0.8299 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8554 (tp) cc_final: 0.7987 (tp) REVERT: A 199 ILE cc_start: 0.8222 (mt) cc_final: 0.7891 (mt) REVERT: A 231 VAL cc_start: 0.8763 (t) cc_final: 0.8183 (p) REVERT: A 235 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7814 (mm-40) REVERT: A 237 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7986 (ttpp) REVERT: A 247 TYR cc_start: 0.7378 (m-10) cc_final: 0.6975 (m-10) REVERT: A 280 ILE cc_start: 0.8988 (mt) cc_final: 0.8755 (tp) REVERT: A 286 LYS cc_start: 0.9149 (tppt) cc_final: 0.8787 (mmmm) REVERT: A 371 TYR cc_start: 0.8057 (m-80) cc_final: 0.7759 (m-80) REVERT: A 383 GLN cc_start: 0.7620 (mt0) cc_final: 0.7363 (mt0) REVERT: A 384 GLU cc_start: 0.6771 (mm-30) cc_final: 0.5954 (mm-30) REVERT: A 395 SER cc_start: 0.8457 (m) cc_final: 0.8097 (p) REVERT: A 398 PHE cc_start: 0.7099 (m-80) cc_final: 0.6495 (m-80) REVERT: A 432 MET cc_start: 0.7510 (tpt) cc_final: 0.6791 (tpt) REVERT: A 447 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7983 (mttp) REVERT: A 473 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7955 (mtpt) REVERT: A 476 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8414 (mtpp) REVERT: A 478 ASP cc_start: 0.8383 (t0) cc_final: 0.7836 (t0) REVERT: A 484 PHE cc_start: 0.8346 (t80) cc_final: 0.7993 (t80) REVERT: A 488 MET cc_start: 0.7678 (tpp) cc_final: 0.7183 (tpp) REVERT: A 530 TYR cc_start: 0.7424 (m-80) cc_final: 0.7154 (m-80) REVERT: A 546 LYS cc_start: 0.8257 (tptm) cc_final: 0.7737 (tptm) REVERT: A 556 TYR cc_start: 0.8186 (p90) cc_final: 0.7882 (p90) REVERT: A 560 ASP cc_start: 0.8207 (m-30) cc_final: 0.7947 (t0) REVERT: A 563 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8100 (ttmm) REVERT: A 662 CYS cc_start: 0.7981 (m) cc_final: 0.7654 (m) REVERT: A 686 ILE cc_start: 0.8731 (pt) cc_final: 0.8445 (mm) REVERT: A 687 ASP cc_start: 0.6948 (t0) cc_final: 0.6500 (t0) REVERT: A 698 ASP cc_start: 0.7676 (t0) cc_final: 0.7453 (t0) REVERT: A 715 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7237 (mmmm) REVERT: A 723 HIS cc_start: 0.7321 (t-170) cc_final: 0.7117 (t-90) REVERT: A 732 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7448 (tp40) REVERT: B 29 GLU cc_start: 0.7095 (mp0) cc_final: 0.6836 (mp0) REVERT: B 103 MET cc_start: 0.5796 (mmt) cc_final: 0.5525 (mmt) REVERT: B 118 TYR cc_start: 0.7241 (m-10) cc_final: 0.6973 (m-80) REVERT: B 134 ARG cc_start: 0.6428 (mtt90) cc_final: 0.6178 (mtt90) REVERT: B 195 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6385 (tp) REVERT: B 199 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7610 (mp) REVERT: B 207 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 213 ARG cc_start: 0.8121 (mtm180) cc_final: 0.7856 (mtm180) REVERT: B 230 GLN cc_start: 0.7941 (tp40) cc_final: 0.7384 (tm-30) REVERT: B 231 VAL cc_start: 0.8649 (p) cc_final: 0.7880 (p) REVERT: B 235 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7305 (mm-40) REVERT: B 236 LEU cc_start: 0.8107 (tp) cc_final: 0.7743 (tp) REVERT: B 237 LYS cc_start: 0.8293 (pttt) cc_final: 0.7876 (pttt) REVERT: B 251 LEU cc_start: 0.8450 (mm) cc_final: 0.6597 (mm) REVERT: B 255 TYR cc_start: 0.8242 (m-10) cc_final: 0.7645 (m-80) REVERT: B 259 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 263 ASN cc_start: 0.7570 (t0) cc_final: 0.7154 (t0) REVERT: B 271 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 286 LYS cc_start: 0.8272 (ttmm) cc_final: 0.8015 (mmmm) REVERT: B 293 LYS cc_start: 0.8578 (pptt) cc_final: 0.7990 (mmmm) REVERT: B 320 GLU cc_start: 0.7656 (tp30) cc_final: 0.7358 (tp30) REVERT: B 359 VAL cc_start: 0.7913 (p) cc_final: 0.7407 (t) REVERT: B 395 SER cc_start: 0.7777 (m) cc_final: 0.7231 (p) REVERT: B 473 LYS cc_start: 0.7998 (mttp) cc_final: 0.6977 (mtpp) REVERT: B 475 ASN cc_start: 0.7892 (t0) cc_final: 0.7534 (t0) REVERT: B 487 ILE cc_start: 0.8588 (pt) cc_final: 0.8343 (mt) REVERT: B 488 MET cc_start: 0.7195 (tpp) cc_final: 0.5841 (tpp) REVERT: B 492 LEU cc_start: 0.8642 (mt) cc_final: 0.7704 (mt) REVERT: B 499 LEU cc_start: 0.8278 (tp) cc_final: 0.8048 (tp) REVERT: B 502 LEU cc_start: 0.8053 (tp) cc_final: 0.7708 (mt) REVERT: B 503 LEU cc_start: 0.8162 (mm) cc_final: 0.7826 (mp) REVERT: B 556 TYR cc_start: 0.8315 (p90) cc_final: 0.8103 (p90) REVERT: B 583 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8713 (tttm) REVERT: B 677 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7100 (ttp80) REVERT: B 682 GLU cc_start: 0.8260 (tp30) cc_final: 0.7760 (tp30) REVERT: B 685 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7584 (ptp90) REVERT: B 687 ASP cc_start: 0.6881 (t0) cc_final: 0.6494 (t0) REVERT: B 701 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6973 (mm-30) REVERT: B 705 GLN cc_start: 0.8364 (tt0) cc_final: 0.8145 (tt0) REVERT: B 706 CYS cc_start: 0.7348 (m) cc_final: 0.7134 (m) outliers start: 53 outliers final: 32 residues processed: 336 average time/residue: 0.2619 time to fit residues: 119.8786 Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 583 LYS 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: 0.7980 chunk 70 optimal weight: 0.0570 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 0.0970 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.116833 restraints weight = 20337.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120645 restraints weight = 11420.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123197 restraints weight = 7296.312| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.189 Angle : 0.606 8.496 14128 Z= 0.313 Chirality : 0.042 0.205 1716 Planarity : 0.004 0.055 1757 Dihedral : 5.811 83.032 1450 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.25 % Allowed : 18.97 % Favored : 75.78 % 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: -1.40 (0.23), residues: 1319 helix: 0.09 (0.18), residues: 822 sheet: -2.25 (0.92), residues: 32 loop : -2.69 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.006 0.001 HIS A 728 PHE 0.021 0.001 PHE A 719 TYR 0.023 0.001 TYR A 105 ARG 0.003 0.000 ARG A 181 *********************** 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 363 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7639 (mm110) cc_final: 0.7429 (mm110) REVERT: A 36 ARG cc_start: 0.7761 (tpp-160) cc_final: 0.7378 (mmt90) REVERT: A 37 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6423 (pm20) REVERT: A 79 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7448 (mmt90) REVERT: A 93 SER cc_start: 0.8492 (t) cc_final: 0.8122 (p) REVERT: A 101 GLN cc_start: 0.7362 (mm110) cc_final: 0.7097 (mm-40) REVERT: A 105 TYR cc_start: 0.7498 (m-80) cc_final: 0.7233 (m-80) REVERT: A 122 PHE cc_start: 0.7275 (m-80) cc_final: 0.6823 (m-10) REVERT: A 123 PRO cc_start: 0.8296 (Cg_exo) cc_final: 0.8043 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8539 (tp) cc_final: 0.7938 (tp) REVERT: A 199 ILE cc_start: 0.8211 (mt) cc_final: 0.7876 (mt) REVERT: A 213 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7298 (mtm-85) REVERT: A 231 VAL cc_start: 0.8776 (t) cc_final: 0.8184 (m) REVERT: A 235 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 237 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8034 (ttpp) REVERT: A 259 GLU cc_start: 0.8180 (tt0) cc_final: 0.7915 (tt0) REVERT: A 271 ASP cc_start: 0.7377 (t0) cc_final: 0.7171 (m-30) REVERT: A 280 ILE cc_start: 0.8976 (mt) cc_final: 0.8747 (tp) REVERT: A 286 LYS cc_start: 0.9150 (tppt) cc_final: 0.8758 (mmmm) REVERT: A 355 SER cc_start: 0.7893 (m) cc_final: 0.7596 (p) REVERT: A 371 TYR cc_start: 0.8067 (m-80) cc_final: 0.7751 (m-80) REVERT: A 383 GLN cc_start: 0.7451 (mt0) cc_final: 0.7184 (mt0) REVERT: A 384 GLU cc_start: 0.6702 (mm-30) cc_final: 0.5910 (mm-30) REVERT: A 395 SER cc_start: 0.8447 (m) cc_final: 0.8065 (p) REVERT: A 398 PHE cc_start: 0.7050 (m-80) cc_final: 0.6498 (m-80) REVERT: A 447 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7921 (mttp) REVERT: A 467 ASP cc_start: 0.7567 (m-30) cc_final: 0.7320 (m-30) REVERT: A 473 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7968 (mtpt) REVERT: A 476 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8438 (mtpp) REVERT: A 478 ASP cc_start: 0.8269 (t0) cc_final: 0.7720 (t0) REVERT: A 484 PHE cc_start: 0.8267 (t80) cc_final: 0.7931 (t80) REVERT: A 488 MET cc_start: 0.7604 (tpp) cc_final: 0.7121 (tpp) REVERT: A 511 LEU cc_start: 0.8843 (mt) cc_final: 0.8619 (mt) REVERT: A 530 TYR cc_start: 0.7419 (m-80) cc_final: 0.7151 (m-80) REVERT: A 546 LYS cc_start: 0.8285 (tptm) cc_final: 0.7745 (tptm) REVERT: A 556 TYR cc_start: 0.8225 (p90) cc_final: 0.7953 (p90) REVERT: A 560 ASP cc_start: 0.8129 (m-30) cc_final: 0.7893 (t0) REVERT: A 563 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8248 (ttmm) REVERT: A 662 CYS cc_start: 0.7898 (m) cc_final: 0.7581 (m) REVERT: A 686 ILE cc_start: 0.8748 (pt) cc_final: 0.8426 (mm) REVERT: A 687 ASP cc_start: 0.6917 (t0) cc_final: 0.6478 (t0) REVERT: A 705 GLN cc_start: 0.8041 (pt0) cc_final: 0.7814 (tt0) REVERT: A 715 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7214 (mmmm) REVERT: A 716 ASP cc_start: 0.7183 (t0) cc_final: 0.6854 (t0) REVERT: B 103 MET cc_start: 0.5811 (mmt) cc_final: 0.5548 (mmp) REVERT: B 118 TYR cc_start: 0.7141 (m-10) cc_final: 0.6910 (m-80) REVERT: B 134 ARG cc_start: 0.6553 (mtt90) cc_final: 0.6343 (mtt90) REVERT: B 158 ASP cc_start: 0.5236 (m-30) cc_final: 0.3655 (m-30) REVERT: B 185 ARG cc_start: 0.6995 (mmt180) cc_final: 0.5797 (mmt180) REVERT: B 192 LEU cc_start: 0.8561 (tp) cc_final: 0.8123 (pp) REVERT: B 195 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6385 (tp) REVERT: B 199 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 207 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 230 GLN cc_start: 0.7852 (tp40) cc_final: 0.7262 (tm-30) REVERT: B 231 VAL cc_start: 0.8650 (p) cc_final: 0.7831 (p) REVERT: B 235 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7257 (mm-40) REVERT: B 236 LEU cc_start: 0.8074 (tp) cc_final: 0.7676 (tp) REVERT: B 237 LYS cc_start: 0.8258 (pttt) cc_final: 0.7830 (pttt) REVERT: B 251 LEU cc_start: 0.8459 (mm) cc_final: 0.6608 (mm) REVERT: B 255 TYR cc_start: 0.8200 (m-10) cc_final: 0.7651 (m-80) REVERT: B 259 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 263 ASN cc_start: 0.7471 (t0) cc_final: 0.6996 (t0) REVERT: B 286 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7805 (tppp) REVERT: B 293 LYS cc_start: 0.8590 (pptt) cc_final: 0.8207 (mmmm) REVERT: B 320 GLU cc_start: 0.7648 (tp30) cc_final: 0.7368 (tp30) REVERT: B 324 ASN cc_start: 0.7691 (t0) cc_final: 0.7316 (t0) REVERT: B 359 VAL cc_start: 0.7913 (p) cc_final: 0.7406 (t) REVERT: B 395 SER cc_start: 0.7755 (m) cc_final: 0.7235 (p) REVERT: B 473 LYS cc_start: 0.7911 (mttp) cc_final: 0.7046 (mtpp) REVERT: B 487 ILE cc_start: 0.8558 (pt) cc_final: 0.8345 (mt) REVERT: B 488 MET cc_start: 0.7138 (tpp) cc_final: 0.5843 (tpp) REVERT: B 492 LEU cc_start: 0.8629 (mt) cc_final: 0.7723 (mt) REVERT: B 499 LEU cc_start: 0.8286 (tp) cc_final: 0.8002 (tp) REVERT: B 502 LEU cc_start: 0.7962 (tp) cc_final: 0.7649 (mt) REVERT: B 556 TYR cc_start: 0.8286 (p90) cc_final: 0.8052 (p90) REVERT: B 677 ARG cc_start: 0.7427 (ttt180) cc_final: 0.7035 (ttp80) REVERT: B 682 GLU cc_start: 0.8263 (tp30) cc_final: 0.7708 (tp30) REVERT: B 685 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7600 (ptp90) REVERT: B 687 ASP cc_start: 0.6876 (t0) cc_final: 0.6451 (t0) REVERT: B 705 GLN cc_start: 0.8348 (tt0) cc_final: 0.8029 (tt0) outliers start: 59 outliers final: 38 residues processed: 339 average time/residue: 0.2500 time to fit residues: 117.3205 Evaluate side-chains 333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 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 304 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 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: 0.3980 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 HIS A 732 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115840 restraints weight = 20256.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.119606 restraints weight = 11378.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.122160 restraints weight = 7235.992| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.197 Angle : 0.629 10.209 14128 Z= 0.322 Chirality : 0.043 0.202 1716 Planarity : 0.004 0.048 1757 Dihedral : 5.866 83.312 1450 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.72 % Allowed : 20.93 % Favored : 74.35 % 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: -1.20 (0.23), residues: 1319 helix: 0.24 (0.18), residues: 823 sheet: -2.46 (0.88), residues: 34 loop : -2.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.011 0.001 HIS A 723 PHE 0.017 0.001 PHE A 385 TYR 0.014 0.001 TYR A 556 ARG 0.004 0.000 ARG A 409 *********************** 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 359 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7462 (mmt90) REVERT: A 37 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6460 (pm20) REVERT: A 93 SER cc_start: 0.8488 (t) cc_final: 0.8118 (p) REVERT: A 101 GLN cc_start: 0.7403 (mm110) cc_final: 0.7136 (mm-40) REVERT: A 105 TYR cc_start: 0.7563 (m-80) cc_final: 0.7297 (m-80) REVERT: A 114 GLN cc_start: 0.7897 (pt0) cc_final: 0.7606 (pt0) REVERT: A 122 PHE cc_start: 0.7286 (m-80) cc_final: 0.6852 (m-10) REVERT: A 123 PRO cc_start: 0.8298 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8507 (tp) cc_final: 0.7981 (tp) REVERT: A 199 ILE cc_start: 0.8225 (mt) cc_final: 0.7880 (mt) REVERT: A 213 ARG cc_start: 0.7538 (mtm180) cc_final: 0.7296 (mtm-85) REVERT: A 231 VAL cc_start: 0.8814 (t) cc_final: 0.8164 (p) REVERT: A 235 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7776 (mm-40) REVERT: A 237 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8065 (ttpp) REVERT: A 280 ILE cc_start: 0.8957 (mt) cc_final: 0.8713 (tp) REVERT: A 286 LYS cc_start: 0.9131 (tppt) cc_final: 0.8784 (mmmm) REVERT: A 355 SER cc_start: 0.7899 (m) cc_final: 0.7594 (p) REVERT: A 371 TYR cc_start: 0.8095 (m-80) cc_final: 0.7760 (m-80) REVERT: A 383 GLN cc_start: 0.7425 (mt0) cc_final: 0.7131 (mt0) REVERT: A 384 GLU cc_start: 0.6716 (mm-30) cc_final: 0.5937 (mm-30) REVERT: A 395 SER cc_start: 0.8474 (m) cc_final: 0.8093 (p) REVERT: A 398 PHE cc_start: 0.7065 (m-80) cc_final: 0.6118 (m-80) REVERT: A 447 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7926 (mttp) REVERT: A 473 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7973 (mtpt) REVERT: A 476 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8518 (mtpp) REVERT: A 478 ASP cc_start: 0.8214 (t0) cc_final: 0.7753 (t0) REVERT: A 484 PHE cc_start: 0.8255 (t80) cc_final: 0.7917 (t80) REVERT: A 488 MET cc_start: 0.7628 (tpp) cc_final: 0.7155 (tpp) REVERT: A 512 ARG cc_start: 0.8649 (mtm110) cc_final: 0.7673 (mtm180) REVERT: A 546 LYS cc_start: 0.8260 (tptm) cc_final: 0.7743 (tptm) REVERT: A 556 TYR cc_start: 0.8236 (p90) cc_final: 0.8012 (p90) REVERT: A 662 CYS cc_start: 0.7748 (m) cc_final: 0.7417 (m) REVERT: A 686 ILE cc_start: 0.8766 (pt) cc_final: 0.8437 (mm) REVERT: A 687 ASP cc_start: 0.7025 (t0) cc_final: 0.6576 (t0) REVERT: A 710 ASP cc_start: 0.7343 (p0) cc_final: 0.7025 (p0) REVERT: A 715 LYS cc_start: 0.7806 (mtpp) cc_final: 0.7152 (mmmm) REVERT: A 716 ASP cc_start: 0.7241 (t0) cc_final: 0.6913 (t0) REVERT: A 723 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7026 (t-90) REVERT: B 29 GLU cc_start: 0.7038 (mp0) cc_final: 0.6706 (mp0) REVERT: B 68 LEU cc_start: 0.8396 (mm) cc_final: 0.8084 (mt) REVERT: B 118 TYR cc_start: 0.7138 (m-10) cc_final: 0.6907 (m-80) REVERT: B 134 ARG cc_start: 0.6496 (mtt90) cc_final: 0.6238 (mtt90) REVERT: B 158 ASP cc_start: 0.5406 (m-30) cc_final: 0.5177 (m-30) REVERT: B 192 LEU cc_start: 0.8557 (tp) cc_final: 0.8121 (pp) REVERT: B 199 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7661 (mp) REVERT: B 207 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 213 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7922 (mtm180) REVERT: B 230 GLN cc_start: 0.7863 (tp40) cc_final: 0.7275 (tm-30) REVERT: B 231 VAL cc_start: 0.8648 (p) cc_final: 0.7851 (p) REVERT: B 235 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7297 (mm-40) REVERT: B 236 LEU cc_start: 0.8069 (tp) cc_final: 0.7684 (tp) REVERT: B 237 LYS cc_start: 0.8226 (pttt) cc_final: 0.7797 (pttt) REVERT: B 251 LEU cc_start: 0.8474 (mm) cc_final: 0.6523 (mm) REVERT: B 255 TYR cc_start: 0.8203 (m-10) cc_final: 0.7666 (m-80) REVERT: B 259 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 263 ASN cc_start: 0.7465 (t0) cc_final: 0.6959 (t0) REVERT: B 286 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7837 (tppp) REVERT: B 320 GLU cc_start: 0.7663 (tp30) cc_final: 0.7389 (tp30) REVERT: B 349 MET cc_start: 0.6897 (mmm) cc_final: 0.6617 (mmp) REVERT: B 395 SER cc_start: 0.7765 (m) cc_final: 0.7235 (p) REVERT: B 473 LYS cc_start: 0.8038 (mttp) cc_final: 0.7309 (mtpp) REVERT: B 475 ASN cc_start: 0.7828 (t0) cc_final: 0.7480 (t0) REVERT: B 488 MET cc_start: 0.7030 (tpp) cc_final: 0.5654 (tpp) REVERT: B 492 LEU cc_start: 0.8578 (mt) cc_final: 0.7445 (mt) REVERT: B 499 LEU cc_start: 0.8265 (tp) cc_final: 0.7964 (tp) REVERT: B 526 SER cc_start: 0.8456 (m) cc_final: 0.8201 (p) REVERT: B 677 ARG cc_start: 0.7420 (ttt180) cc_final: 0.7049 (ttp80) REVERT: B 682 GLU cc_start: 0.8283 (tp30) cc_final: 0.7693 (tp30) REVERT: B 685 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7638 (ptp90) REVERT: B 687 ASP cc_start: 0.6941 (t0) cc_final: 0.6565 (t0) REVERT: B 705 GLN cc_start: 0.8363 (tt0) cc_final: 0.8061 (tt0) REVERT: B 724 ASP cc_start: 0.7191 (m-30) cc_final: 0.6852 (m-30) outliers start: 53 outliers final: 39 residues processed: 335 average time/residue: 0.2545 time to fit residues: 117.1263 Evaluate side-chains 338 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 303 GLU Chi-restraints excluded: chain A residue 349 MET 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 723 HIS 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 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 333 SER 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 685 ARG 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: 3.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 32 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 HIS A 732 GLN B 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114367 restraints weight = 20453.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118167 restraints weight = 11534.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120708 restraints weight = 7307.008| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10395 Z= 0.229 Angle : 0.650 14.929 14128 Z= 0.334 Chirality : 0.044 0.248 1716 Planarity : 0.004 0.052 1757 Dihedral : 5.920 85.984 1448 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.16 % Allowed : 21.73 % Favored : 73.11 % 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: -1.14 (0.23), residues: 1319 helix: 0.31 (0.18), residues: 815 sheet: -2.51 (0.87), residues: 34 loop : -2.56 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.011 0.001 HIS A 728 PHE 0.025 0.001 PHE A 130 TYR 0.013 0.001 TYR B 361 ARG 0.005 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 1.117 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: 0.7894 (tpp-160) cc_final: 0.7617 (mmt90) REVERT: A 37 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: A 79 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7472 (mmt90) REVERT: A 93 SER cc_start: 0.8481 (t) cc_final: 0.8132 (p) REVERT: A 101 GLN cc_start: 0.7431 (mm110) cc_final: 0.7106 (mm-40) REVERT: A 105 TYR cc_start: 0.7597 (m-80) cc_final: 0.7293 (m-80) REVERT: A 114 GLN cc_start: 0.7955 (pt0) cc_final: 0.7669 (pt0) REVERT: A 122 PHE cc_start: 0.7255 (m-80) cc_final: 0.6726 (m-10) REVERT: A 123 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8581 (tp) cc_final: 0.8109 (tp) REVERT: A 199 ILE cc_start: 0.8241 (mt) cc_final: 0.7908 (mt) REVERT: A 231 VAL cc_start: 0.8780 (t) cc_final: 0.8118 (p) REVERT: A 234 SER cc_start: 0.8769 (m) cc_final: 0.8310 (t) REVERT: A 235 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 237 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8149 (ttpp) REVERT: A 280 ILE cc_start: 0.8961 (mt) cc_final: 0.8742 (tp) REVERT: A 286 LYS cc_start: 0.9155 (tppt) cc_final: 0.8767 (mmmm) REVERT: A 304 VAL cc_start: 0.9000 (t) cc_final: 0.8547 (p) REVERT: A 307 THR cc_start: 0.8495 (m) cc_final: 0.8239 (p) REVERT: A 335 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6901 (t80) REVERT: A 371 TYR cc_start: 0.8151 (m-80) cc_final: 0.7857 (m-80) REVERT: A 383 GLN cc_start: 0.7386 (mt0) cc_final: 0.7128 (mt0) REVERT: A 384 GLU cc_start: 0.6698 (mm-30) cc_final: 0.5938 (mm-30) REVERT: A 395 SER cc_start: 0.8467 (m) cc_final: 0.8104 (p) REVERT: A 398 PHE cc_start: 0.7047 (m-80) cc_final: 0.6488 (m-80) REVERT: A 447 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7919 (mttp) REVERT: A 473 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 476 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8494 (mtpp) REVERT: A 478 ASP cc_start: 0.8129 (t0) cc_final: 0.7677 (t0) REVERT: A 484 PHE cc_start: 0.8257 (t80) cc_final: 0.7940 (t80) REVERT: A 488 MET cc_start: 0.7605 (tpp) cc_final: 0.7165 (tpp) REVERT: A 512 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8163 (mtt90) REVERT: A 546 LYS cc_start: 0.8232 (tptm) cc_final: 0.7717 (tptm) REVERT: A 662 CYS cc_start: 0.7874 (m) cc_final: 0.7577 (m) REVERT: A 686 ILE cc_start: 0.8799 (pt) cc_final: 0.7797 (mm) REVERT: A 705 GLN cc_start: 0.8038 (pt0) cc_final: 0.7777 (tt0) REVERT: A 710 ASP cc_start: 0.7369 (p0) cc_final: 0.6737 (p0) REVERT: A 715 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7209 (mmmm) REVERT: A 716 ASP cc_start: 0.7256 (t0) cc_final: 0.7029 (t0) REVERT: A 723 HIS cc_start: 0.7455 (t-90) cc_final: 0.7119 (t-90) REVERT: B 68 LEU cc_start: 0.8409 (mm) cc_final: 0.8068 (mt) REVERT: B 134 ARG cc_start: 0.6513 (mtt90) cc_final: 0.6294 (mtt90) REVERT: B 207 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 230 GLN cc_start: 0.7877 (tp40) cc_final: 0.7282 (tm-30) REVERT: B 231 VAL cc_start: 0.8648 (p) cc_final: 0.8170 (p) REVERT: B 236 LEU cc_start: 0.8016 (tp) cc_final: 0.7593 (tp) REVERT: B 237 LYS cc_start: 0.8224 (pttt) cc_final: 0.7792 (pttt) REVERT: B 251 LEU cc_start: 0.8479 (mm) cc_final: 0.6540 (mm) REVERT: B 255 TYR cc_start: 0.8191 (m-10) cc_final: 0.7694 (m-80) REVERT: B 259 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 263 ASN cc_start: 0.7422 (t0) cc_final: 0.6800 (t0) REVERT: B 271 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7472 (p0) REVERT: B 286 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7820 (tppp) REVERT: B 293 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8031 (mmtm) REVERT: B 320 GLU cc_start: 0.7657 (tp30) cc_final: 0.7413 (tp30) REVERT: B 324 ASN cc_start: 0.7718 (t0) cc_final: 0.7417 (t0) REVERT: B 340 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7165 (pp) REVERT: B 395 SER cc_start: 0.7886 (m) cc_final: 0.7320 (p) REVERT: B 473 LYS cc_start: 0.8058 (mttp) cc_final: 0.7196 (mtpp) REVERT: B 488 MET cc_start: 0.6973 (tpp) cc_final: 0.5616 (tpp) REVERT: B 492 LEU cc_start: 0.8659 (mt) cc_final: 0.7470 (mt) REVERT: B 499 LEU cc_start: 0.8213 (tp) cc_final: 0.7910 (tp) REVERT: B 526 SER cc_start: 0.8532 (m) cc_final: 0.8307 (p) REVERT: B 677 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7074 (ttp80) REVERT: B 682 GLU cc_start: 0.8297 (tp30) cc_final: 0.7924 (tp30) REVERT: B 705 GLN cc_start: 0.8317 (tt0) cc_final: 0.7992 (tt0) REVERT: B 720 LEU cc_start: 0.8520 (mp) cc_final: 0.8240 (mp) REVERT: B 724 ASP cc_start: 0.7298 (m-30) cc_final: 0.6991 (m-30) outliers start: 58 outliers final: 39 residues processed: 333 average time/residue: 0.2479 time to fit residues: 113.1554 Evaluate side-chains 333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 335 PHE Chi-restraints excluded: chain A residue 349 MET 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 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 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 462 PHE 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 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 728 HIS A 732 GLN B 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.132364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113466 restraints weight = 20707.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117306 restraints weight = 11685.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119860 restraints weight = 7371.722| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4542 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= 0.233 Angle : 0.663 11.257 14128 Z= 0.341 Chirality : 0.044 0.227 1716 Planarity : 0.004 0.051 1757 Dihedral : 5.434 52.776 1443 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.08 % Allowed : 22.08 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.14 (0.23), residues: 1319 helix: 0.28 (0.18), residues: 821 sheet: -2.60 (0.86), residues: 34 loop : -2.50 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.009 0.001 HIS A 723 PHE 0.030 0.001 PHE A 130 TYR 0.033 0.002 TYR A 556 ARG 0.003 0.000 ARG A 181 *********************** 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 363 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7597 (mmt90) REVERT: A 37 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6522 (pm20) REVERT: A 79 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7324 (mmt90) REVERT: A 93 SER cc_start: 0.8473 (t) cc_final: 0.8152 (p) REVERT: A 101 GLN cc_start: 0.7332 (mm110) cc_final: 0.7122 (mm-40) REVERT: A 105 TYR cc_start: 0.7588 (m-80) cc_final: 0.7326 (m-80) REVERT: A 114 GLN cc_start: 0.7969 (pt0) cc_final: 0.7688 (pt0) REVERT: A 122 PHE cc_start: 0.7177 (m-80) cc_final: 0.6729 (m-10) REVERT: A 123 PRO cc_start: 0.8277 (Cg_exo) cc_final: 0.8020 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8600 (tp) cc_final: 0.8118 (tp) REVERT: A 199 ILE cc_start: 0.8227 (mt) cc_final: 0.7887 (mt) REVERT: A 231 VAL cc_start: 0.8744 (t) cc_final: 0.8058 (p) REVERT: A 234 SER cc_start: 0.8764 (m) cc_final: 0.8228 (t) REVERT: A 235 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7692 (mm-40) REVERT: A 237 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8169 (ttpp) REVERT: A 240 LEU cc_start: 0.8421 (mm) cc_final: 0.8152 (mp) REVERT: A 276 LEU cc_start: 0.8502 (mm) cc_final: 0.8244 (mm) REVERT: A 280 ILE cc_start: 0.8925 (mt) cc_final: 0.8700 (tp) REVERT: A 286 LYS cc_start: 0.9124 (tppt) cc_final: 0.8736 (mmmm) REVERT: A 304 VAL cc_start: 0.8978 (t) cc_final: 0.8678 (p) REVERT: A 306 VAL cc_start: 0.8992 (p) cc_final: 0.8772 (m) REVERT: A 335 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6832 (t80) REVERT: A 395 SER cc_start: 0.8484 (m) cc_final: 0.8133 (p) REVERT: A 398 PHE cc_start: 0.7031 (m-80) cc_final: 0.6499 (m-80) REVERT: A 447 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7884 (mttp) REVERT: A 457 ASN cc_start: 0.8104 (m110) cc_final: 0.7609 (m110) REVERT: A 473 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7867 (mtpt) REVERT: A 476 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8487 (mtpp) REVERT: A 478 ASP cc_start: 0.7990 (t0) cc_final: 0.7541 (t0) REVERT: A 484 PHE cc_start: 0.8214 (t80) cc_final: 0.7917 (t80) REVERT: A 488 MET cc_start: 0.7539 (tpp) cc_final: 0.7067 (tpp) REVERT: A 511 LEU cc_start: 0.8904 (mt) cc_final: 0.8702 (mm) REVERT: A 512 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8325 (ttm110) REVERT: A 546 LYS cc_start: 0.8216 (tptm) cc_final: 0.7720 (tptm) REVERT: A 662 CYS cc_start: 0.7862 (m) cc_final: 0.7577 (m) REVERT: A 667 PHE cc_start: 0.7761 (p90) cc_final: 0.7443 (p90) REVERT: A 684 GLN cc_start: 0.7497 (tp40) cc_final: 0.7184 (tp40) REVERT: A 705 GLN cc_start: 0.8023 (pt0) cc_final: 0.7777 (tt0) REVERT: A 715 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7214 (mmmm) REVERT: A 716 ASP cc_start: 0.7229 (t0) cc_final: 0.7003 (t0) REVERT: A 723 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.7017 (t-90) REVERT: A 730 GLN cc_start: 0.8557 (mt0) cc_final: 0.8325 (mt0) REVERT: B 68 LEU cc_start: 0.8425 (mm) cc_final: 0.8058 (mt) REVERT: B 158 ASP cc_start: 0.5684 (m-30) cc_final: 0.4792 (m-30) REVERT: B 185 ARG cc_start: 0.7256 (mmt180) cc_final: 0.6434 (mmt180) REVERT: B 207 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 230 GLN cc_start: 0.7850 (tp40) cc_final: 0.7344 (tm-30) REVERT: B 231 VAL cc_start: 0.8687 (p) cc_final: 0.8255 (p) REVERT: B 236 LEU cc_start: 0.8075 (tp) cc_final: 0.7554 (tp) REVERT: B 237 LYS cc_start: 0.8189 (pttt) cc_final: 0.7766 (pttt) REVERT: B 251 LEU cc_start: 0.8448 (mm) cc_final: 0.6546 (mm) REVERT: B 255 TYR cc_start: 0.8131 (m-10) cc_final: 0.7682 (m-80) REVERT: B 259 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 263 ASN cc_start: 0.7319 (t0) cc_final: 0.6736 (t0) REVERT: B 271 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7430 (p0) REVERT: B 293 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8158 (mmtm) REVERT: B 320 GLU cc_start: 0.7584 (tp30) cc_final: 0.7343 (tp30) REVERT: B 324 ASN cc_start: 0.7816 (t0) cc_final: 0.7538 (t0) REVERT: B 340 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6902 (pp) REVERT: B 395 SER cc_start: 0.8066 (m) cc_final: 0.7525 (p) REVERT: B 473 LYS cc_start: 0.8079 (mttp) cc_final: 0.7233 (mtpp) REVERT: B 475 ASN cc_start: 0.7959 (t0) cc_final: 0.7590 (t0) REVERT: B 488 MET cc_start: 0.6872 (tpp) cc_final: 0.5568 (tpp) REVERT: B 492 LEU cc_start: 0.8646 (mt) cc_final: 0.7495 (mt) REVERT: B 499 LEU cc_start: 0.8206 (tp) cc_final: 0.7912 (tp) REVERT: B 526 SER cc_start: 0.8578 (m) cc_final: 0.8346 (p) REVERT: B 677 ARG cc_start: 0.7366 (ttt180) cc_final: 0.7071 (ttp80) REVERT: B 681 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8028 (ttpp) REVERT: B 682 GLU cc_start: 0.8215 (tp30) cc_final: 0.7823 (tp30) REVERT: B 705 GLN cc_start: 0.8279 (tt0) cc_final: 0.7779 (pp30) REVERT: B 724 ASP cc_start: 0.7314 (m-30) cc_final: 0.7045 (m-30) outliers start: 57 outliers final: 48 residues processed: 340 average time/residue: 0.2431 time to fit residues: 113.3254 Evaluate side-chains 348 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 272 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU 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 495 ASP 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 A residue 723 HIS 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 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: 0.0020 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 728 HIS A 732 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.131816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113012 restraints weight = 20578.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116783 restraints weight = 11612.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119325 restraints weight = 7353.906| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10395 Z= 0.230 Angle : 0.683 11.138 14128 Z= 0.349 Chirality : 0.045 0.283 1716 Planarity : 0.005 0.052 1757 Dihedral : 5.466 52.699 1443 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 5.34 % Allowed : 22.17 % Favored : 72.48 % 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: -1.03 (0.24), residues: 1319 helix: 0.35 (0.18), residues: 809 sheet: -2.65 (0.96), residues: 28 loop : -2.36 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.008 0.001 HIS A 723 PHE 0.032 0.001 PHE A 210 TYR 0.031 0.002 TYR A 556 ARG 0.003 0.000 ARG B 213 *********************** 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 349 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 0.957 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 36 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7649 (mmt90) REVERT: A 37 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6506 (pm20) REVERT: A 79 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7394 (mmt90) REVERT: A 93 SER cc_start: 0.8482 (t) cc_final: 0.8170 (p) REVERT: A 101 GLN cc_start: 0.7316 (mm110) cc_final: 0.7095 (mm-40) REVERT: A 105 TYR cc_start: 0.7541 (m-80) cc_final: 0.7327 (m-80) REVERT: A 122 PHE cc_start: 0.7181 (m-80) cc_final: 0.6736 (m-10) REVERT: A 123 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8631 (tp) cc_final: 0.8138 (tp) REVERT: A 199 ILE cc_start: 0.8177 (mt) cc_final: 0.7842 (mt) REVERT: A 231 VAL cc_start: 0.8726 (t) cc_final: 0.8051 (p) REVERT: A 234 SER cc_start: 0.8765 (m) cc_final: 0.8200 (t) REVERT: A 235 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7705 (mm-40) REVERT: A 237 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8182 (ttpp) REVERT: A 240 LEU cc_start: 0.8432 (mm) cc_final: 0.8145 (mp) REVERT: A 276 LEU cc_start: 0.8492 (mm) cc_final: 0.8134 (mm) REVERT: A 286 LYS cc_start: 0.9122 (tppt) cc_final: 0.8816 (tppt) REVERT: A 304 VAL cc_start: 0.8999 (t) cc_final: 0.8709 (p) REVERT: A 306 VAL cc_start: 0.9000 (p) cc_final: 0.8781 (m) REVERT: A 335 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 371 TYR cc_start: 0.8119 (m-80) cc_final: 0.7775 (m-80) REVERT: A 383 GLN cc_start: 0.7126 (mt0) cc_final: 0.6920 (mp10) REVERT: A 395 SER cc_start: 0.8503 (m) cc_final: 0.8146 (p) REVERT: A 457 ASN cc_start: 0.8132 (m110) cc_final: 0.7665 (m-40) REVERT: A 473 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7885 (mtpt) REVERT: A 476 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8517 (mmmt) REVERT: A 478 ASP cc_start: 0.7978 (t0) cc_final: 0.7535 (t0) REVERT: A 484 PHE cc_start: 0.8198 (t80) cc_final: 0.7887 (t80) REVERT: A 488 MET cc_start: 0.7518 (tpp) cc_final: 0.7038 (tpp) REVERT: A 511 LEU cc_start: 0.8865 (mt) cc_final: 0.8637 (mm) REVERT: A 546 LYS cc_start: 0.8225 (tptm) cc_final: 0.7684 (tptm) REVERT: A 662 CYS cc_start: 0.7847 (m) cc_final: 0.7570 (m) REVERT: A 667 PHE cc_start: 0.7754 (p90) cc_final: 0.7448 (p90) REVERT: A 715 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7594 (mtmm) REVERT: A 716 ASP cc_start: 0.7239 (t0) cc_final: 0.7005 (t0) REVERT: A 723 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: B 68 LEU cc_start: 0.8399 (mm) cc_final: 0.8035 (mt) REVERT: B 134 ARG cc_start: 0.6383 (mtt90) cc_final: 0.6075 (mtt90) REVERT: B 207 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 230 GLN cc_start: 0.7827 (tp40) cc_final: 0.7301 (tm-30) REVERT: B 231 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 236 LEU cc_start: 0.8074 (tp) cc_final: 0.7702 (tp) REVERT: B 237 LYS cc_start: 0.8160 (pttt) cc_final: 0.7752 (pttt) REVERT: B 251 LEU cc_start: 0.8452 (mm) cc_final: 0.6595 (mm) REVERT: B 255 TYR cc_start: 0.8145 (m-10) cc_final: 0.7672 (m-80) REVERT: B 259 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 263 ASN cc_start: 0.7229 (t0) cc_final: 0.6679 (t0) REVERT: B 271 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7448 (p0) REVERT: B 293 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8153 (mmtm) REVERT: B 320 GLU cc_start: 0.7612 (tp30) cc_final: 0.7360 (tp30) REVERT: B 324 ASN cc_start: 0.7932 (t0) cc_final: 0.7624 (t0) REVERT: B 340 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7245 (pp) REVERT: B 395 SER cc_start: 0.8057 (m) cc_final: 0.7518 (p) REVERT: B 473 LYS cc_start: 0.8006 (mttp) cc_final: 0.7270 (ttpp) REVERT: B 475 ASN cc_start: 0.7935 (t0) cc_final: 0.7635 (t0) REVERT: B 488 MET cc_start: 0.6915 (tpp) cc_final: 0.5430 (tpp) REVERT: B 492 LEU cc_start: 0.8653 (mt) cc_final: 0.7437 (mt) REVERT: B 499 LEU cc_start: 0.8234 (tp) cc_final: 0.7935 (tp) REVERT: B 677 ARG cc_start: 0.7371 (ttt180) cc_final: 0.7077 (ttp80) REVERT: B 681 LYS cc_start: 0.8430 (ptmm) cc_final: 0.8035 (ttpp) REVERT: B 682 GLU cc_start: 0.8178 (tp30) cc_final: 0.7833 (tp30) REVERT: B 705 GLN cc_start: 0.8279 (tt0) cc_final: 0.7804 (pp30) REVERT: B 720 LEU cc_start: 0.8427 (mp) cc_final: 0.8208 (mp) REVERT: B 724 ASP cc_start: 0.7197 (m-30) cc_final: 0.6931 (m-30) outliers start: 60 outliers final: 48 residues processed: 326 average time/residue: 0.2350 time to fit residues: 105.7325 Evaluate side-chains 346 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 113 VAL 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 272 PHE Chi-restraints excluded: chain A residue 335 PHE 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 495 ASP 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 723 HIS 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 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.0070 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 96 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 728 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.115047 restraints weight = 20459.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.118851 restraints weight = 11569.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121427 restraints weight = 7339.687| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10395 Z= 0.194 Angle : 0.676 9.559 14128 Z= 0.343 Chirality : 0.044 0.357 1716 Planarity : 0.004 0.047 1757 Dihedral : 5.390 52.347 1443 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 4.99 % Allowed : 22.80 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1319 helix: 0.40 (0.18), residues: 811 sheet: -2.51 (0.99), residues: 28 loop : -2.35 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 482 HIS 0.009 0.001 HIS A 723 PHE 0.027 0.001 PHE A 719 TYR 0.029 0.002 TYR A 556 ARG 0.012 0.001 ARG A 213 *********************** 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 343 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 1.052 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: A 36 ARG cc_start: 0.7845 (tpp-160) cc_final: 0.7611 (mmt90) REVERT: A 37 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: A 79 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7386 (mmt90) REVERT: A 93 SER cc_start: 0.8461 (t) cc_final: 0.8124 (p) REVERT: A 122 PHE cc_start: 0.7160 (m-80) cc_final: 0.6759 (m-10) REVERT: A 123 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8545 (tp) cc_final: 0.8000 (tp) REVERT: A 199 ILE cc_start: 0.8134 (mt) cc_final: 0.7799 (mt) REVERT: A 206 LEU cc_start: 0.7995 (mt) cc_final: 0.7667 (mt) REVERT: A 231 VAL cc_start: 0.8720 (t) cc_final: 0.7995 (p) REVERT: A 235 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 237 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8108 (ttpp) REVERT: A 240 LEU cc_start: 0.8388 (mm) cc_final: 0.8137 (mp) REVERT: A 276 LEU cc_start: 0.8520 (mm) cc_final: 0.8188 (mm) REVERT: A 280 ILE cc_start: 0.8932 (mt) cc_final: 0.8701 (tp) REVERT: A 286 LYS cc_start: 0.9122 (tppt) cc_final: 0.8756 (mmmm) REVERT: A 304 VAL cc_start: 0.8984 (t) cc_final: 0.8685 (p) REVERT: A 306 VAL cc_start: 0.8999 (p) cc_final: 0.8777 (m) REVERT: A 355 SER cc_start: 0.7827 (m) cc_final: 0.7514 (p) REVERT: A 371 TYR cc_start: 0.8024 (m-80) cc_final: 0.7717 (m-80) REVERT: A 395 SER cc_start: 0.8452 (m) cc_final: 0.8098 (p) REVERT: A 438 LEU cc_start: 0.7760 (tp) cc_final: 0.7540 (tp) REVERT: A 447 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7806 (mttp) REVERT: A 457 ASN cc_start: 0.8081 (m110) cc_final: 0.7628 (m-40) REVERT: A 473 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7823 (mtpt) REVERT: A 476 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8307 (mtpp) REVERT: A 488 MET cc_start: 0.7477 (tpp) cc_final: 0.6967 (tpp) REVERT: A 537 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7912 (mttm) REVERT: A 546 LYS cc_start: 0.8243 (tptm) cc_final: 0.7730 (tptm) REVERT: A 662 CYS cc_start: 0.7717 (m) cc_final: 0.7448 (m) REVERT: A 667 PHE cc_start: 0.7698 (p90) cc_final: 0.7440 (p90) REVERT: A 681 LYS cc_start: 0.8023 (tptt) cc_final: 0.7009 (tptt) REVERT: A 715 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7099 (mmmm) REVERT: A 716 ASP cc_start: 0.7256 (t0) cc_final: 0.6963 (t0) REVERT: B 68 LEU cc_start: 0.8369 (mm) cc_final: 0.8000 (mt) REVERT: B 134 ARG cc_start: 0.6381 (mtt90) cc_final: 0.6097 (mtt90) REVERT: B 207 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 230 GLN cc_start: 0.7790 (tp40) cc_final: 0.7394 (tm-30) REVERT: B 231 VAL cc_start: 0.8669 (p) cc_final: 0.8318 (p) REVERT: B 236 LEU cc_start: 0.8011 (tp) cc_final: 0.7662 (tp) REVERT: B 237 LYS cc_start: 0.8096 (pttt) cc_final: 0.7603 (pttp) REVERT: B 251 LEU cc_start: 0.8418 (mm) cc_final: 0.6548 (mm) REVERT: B 255 TYR cc_start: 0.8120 (m-10) cc_final: 0.7666 (m-80) REVERT: B 259 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 263 ASN cc_start: 0.7265 (t0) cc_final: 0.6756 (t0) REVERT: B 271 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7390 (p0) REVERT: B 293 LYS cc_start: 0.8462 (mmmm) cc_final: 0.8073 (mmtm) REVERT: B 320 GLU cc_start: 0.7544 (tp30) cc_final: 0.7300 (tp30) REVERT: B 324 ASN cc_start: 0.7895 (t0) cc_final: 0.7604 (t0) REVERT: B 340 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7217 (pp) REVERT: B 395 SER cc_start: 0.7827 (m) cc_final: 0.7289 (p) REVERT: B 473 LYS cc_start: 0.8057 (mttp) cc_final: 0.7604 (ttpp) REVERT: B 475 ASN cc_start: 0.7948 (t0) cc_final: 0.7684 (t0) REVERT: B 488 MET cc_start: 0.6884 (tpp) cc_final: 0.5498 (tpp) REVERT: B 492 LEU cc_start: 0.8653 (mt) cc_final: 0.7544 (mt) REVERT: B 499 LEU cc_start: 0.8215 (tp) cc_final: 0.7933 (tp) REVERT: B 681 LYS cc_start: 0.8429 (ptmm) cc_final: 0.8056 (ttpp) REVERT: B 682 GLU cc_start: 0.8152 (tp30) cc_final: 0.7781 (tp30) REVERT: B 705 GLN cc_start: 0.8261 (tt0) cc_final: 0.7763 (pp30) REVERT: B 720 LEU cc_start: 0.8504 (mp) cc_final: 0.8232 (mp) REVERT: B 724 ASP cc_start: 0.7262 (m-30) cc_final: 0.6988 (m-30) outliers start: 56 outliers final: 47 residues processed: 321 average time/residue: 0.2336 time to fit residues: 103.0978 Evaluate side-chains 328 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 113 VAL 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 207 GLN 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 335 PHE 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 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 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 155 MET 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 513 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.0060 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 446 GLN A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.134275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115073 restraints weight = 20607.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.118946 restraints weight = 11656.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121524 restraints weight = 7379.381| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10395 Z= 0.201 Angle : 0.698 9.378 14128 Z= 0.354 Chirality : 0.045 0.398 1716 Planarity : 0.004 0.048 1757 Dihedral : 5.396 52.600 1443 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 4.72 % Allowed : 23.33 % 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: -0.92 (0.23), residues: 1319 helix: 0.44 (0.18), residues: 798 sheet: -2.37 (1.02), residues: 28 loop : -2.28 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 482 HIS 0.008 0.001 HIS A 728 PHE 0.023 0.001 PHE A 210 TYR 0.037 0.002 TYR A 530 ARG 0.007 0.000 ARG B 213 ********************** 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 335 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 1.272 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: A 36 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7627 (mmt90) REVERT: A 37 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: A 79 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7396 (mmt90) REVERT: A 93 SER cc_start: 0.8465 (t) cc_final: 0.8135 (p) REVERT: A 122 PHE cc_start: 0.7162 (m-80) cc_final: 0.6751 (m-10) REVERT: A 123 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7922 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8561 (tp) cc_final: 0.7997 (tp) REVERT: A 199 ILE cc_start: 0.8068 (mt) cc_final: 0.7720 (mt) REVERT: A 206 LEU cc_start: 0.7958 (mt) cc_final: 0.7629 (mt) REVERT: A 231 VAL cc_start: 0.8728 (t) cc_final: 0.7995 (p) REVERT: A 235 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7743 (mm-40) REVERT: A 237 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8084 (ttpp) REVERT: A 240 LEU cc_start: 0.8382 (mm) cc_final: 0.8137 (mp) REVERT: A 276 LEU cc_start: 0.8529 (mm) cc_final: 0.8204 (mm) REVERT: A 280 ILE cc_start: 0.8949 (mt) cc_final: 0.8699 (tp) REVERT: A 286 LYS cc_start: 0.9147 (tppt) cc_final: 0.8782 (mmmm) REVERT: A 304 VAL cc_start: 0.8989 (t) cc_final: 0.8692 (p) REVERT: A 306 VAL cc_start: 0.8991 (p) cc_final: 0.8773 (m) REVERT: A 355 SER cc_start: 0.7841 (m) cc_final: 0.7528 (p) REVERT: A 371 TYR cc_start: 0.8025 (m-80) cc_final: 0.7690 (m-80) REVERT: A 395 SER cc_start: 0.8409 (m) cc_final: 0.8080 (p) REVERT: A 438 LEU cc_start: 0.7788 (tp) cc_final: 0.7568 (tp) REVERT: A 447 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7802 (mttp) REVERT: A 457 ASN cc_start: 0.8048 (m110) cc_final: 0.7592 (m-40) REVERT: A 473 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7779 (mtpt) REVERT: A 476 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8379 (mtpp) REVERT: A 488 MET cc_start: 0.7508 (tpp) cc_final: 0.7025 (tpp) REVERT: A 537 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7903 (mttm) REVERT: A 546 LYS cc_start: 0.8248 (tptm) cc_final: 0.7745 (tptm) REVERT: A 662 CYS cc_start: 0.7712 (m) cc_final: 0.7483 (m) REVERT: A 667 PHE cc_start: 0.7681 (p90) cc_final: 0.7417 (p90) REVERT: A 681 LYS cc_start: 0.8028 (tptt) cc_final: 0.7014 (tptt) REVERT: A 715 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7091 (mmmm) REVERT: A 716 ASP cc_start: 0.7272 (t0) cc_final: 0.6969 (t0) REVERT: B 68 LEU cc_start: 0.8364 (mm) cc_final: 0.7992 (mt) REVERT: B 134 ARG cc_start: 0.6395 (mtt90) cc_final: 0.6114 (mtt90) REVERT: B 207 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 230 GLN cc_start: 0.7847 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 231 VAL cc_start: 0.8694 (p) cc_final: 0.8306 (p) REVERT: B 236 LEU cc_start: 0.8077 (tp) cc_final: 0.7678 (tp) REVERT: B 237 LYS cc_start: 0.8129 (pttt) cc_final: 0.7765 (pttt) REVERT: B 251 LEU cc_start: 0.8412 (mm) cc_final: 0.6550 (mm) REVERT: B 255 TYR cc_start: 0.8135 (m-10) cc_final: 0.7666 (m-80) REVERT: B 259 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 263 ASN cc_start: 0.7281 (t0) cc_final: 0.6828 (t0) REVERT: B 293 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8132 (mptt) REVERT: B 320 GLU cc_start: 0.7491 (tp30) cc_final: 0.7252 (tp30) REVERT: B 324 ASN cc_start: 0.7820 (t0) cc_final: 0.7551 (t0) REVERT: B 340 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7222 (pp) REVERT: B 395 SER cc_start: 0.7814 (m) cc_final: 0.7283 (p) REVERT: B 462 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 473 LYS cc_start: 0.8076 (mttp) cc_final: 0.7580 (ttpp) REVERT: B 488 MET cc_start: 0.6908 (tpp) cc_final: 0.5632 (tpp) REVERT: B 492 LEU cc_start: 0.8659 (mt) cc_final: 0.7525 (mt) REVERT: B 499 LEU cc_start: 0.8177 (tp) cc_final: 0.7907 (tp) REVERT: B 681 LYS cc_start: 0.8445 (ptmm) cc_final: 0.8065 (ttpp) REVERT: B 682 GLU cc_start: 0.8158 (tp30) cc_final: 0.7760 (tp30) REVERT: B 705 GLN cc_start: 0.8261 (tt0) cc_final: 0.7757 (pp30) REVERT: B 720 LEU cc_start: 0.8493 (mp) cc_final: 0.8160 (mt) REVERT: B 724 ASP cc_start: 0.7123 (m-30) cc_final: 0.6882 (m-30) outliers start: 53 outliers final: 45 residues processed: 315 average time/residue: 0.2434 time to fit residues: 105.6331 Evaluate side-chains 342 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE 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 461 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP 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 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 264 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 446 GLN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112555 restraints weight = 20579.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116327 restraints weight = 11644.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118859 restraints weight = 7406.585| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.5037 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= 0.240 Angle : 0.729 15.477 14128 Z= 0.370 Chirality : 0.046 0.372 1716 Planarity : 0.005 0.053 1757 Dihedral : 5.516 52.890 1443 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 3.92 % Allowed : 24.84 % 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: -0.95 (0.23), residues: 1319 helix: 0.41 (0.18), residues: 798 sheet: -2.47 (1.01), residues: 28 loop : -2.27 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 83 HIS 0.007 0.001 HIS A 723 PHE 0.024 0.001 PHE A 550 TYR 0.028 0.002 TYR A 556 ARG 0.011 0.001 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3654.19 seconds wall clock time: 66 minutes 21.61 seconds (3981.61 seconds total)