Starting phenix.real_space_refine on Wed Mar 4 02:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wla_32579/03_2026/7wla_32579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wla_32579/03_2026/7wla_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_32579/03_2026/7wla_32579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wla_32579/03_2026/7wla_32579.map" model { file = "/net/cci-nas-00/data/ceres_data/7wla_32579/03_2026/7wla_32579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wla_32579/03_2026/7wla_32579.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.21, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 545.8 milliseconds 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: 0.31 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: 1.59 Time building geometry restraints manager: 1.08 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10395 Z= 0.091 Angle : 0.445 5.469 14128 Z= 0.251 Chirality : 0.037 0.130 1716 Planarity : 0.003 0.043 1757 Dihedral : 8.816 88.787 3714 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.01 % Allowed : 5.52 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 512 TYR 0.005 0.001 TYR A 377 PHE 0.008 0.001 PHE A 555 TRP 0.005 0.000 TRP B 83 HIS 0.001 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00169 (10395) covalent geometry : angle 0.44482 (14128) hydrogen bonds : bond 0.23262 ( 544) hydrogen bonds : angle 6.79140 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.240 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: 0.8254 (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: 0.8347 (ttpp) cc_final: 0.7839 (ttpp) REVERT: A 260 ILE cc_start: 0.8844 (mt) cc_final: 0.8503 (tp) REVERT: A 272 PHE cc_start: 0.7780 (t80) cc_final: 0.7542 (t80) REVERT: A 280 ILE cc_start: 0.8879 (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: 0.6472 (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: 0.7135 (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: 0.8239 (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: 0.6782 (t-90) REVERT: B 48 ASP cc_start: 0.6067 (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: 0.8018 (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: 0.6324 (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: 0.7427 (tp30) REVERT: B 371 TYR cc_start: 0.7104 (m-80) cc_final: 0.6726 (m-80) REVERT: B 375 HIS cc_start: 0.6368 (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: 0.6766 (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: 0.7397 (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: 0.5729 (OUTLIER) cc_final: 0.4755 (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: 0.1101 time to fit residues: 61.0229 Evaluate side-chains 331 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0070 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 730 GLN A 732 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 289 ASN 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 = 0.4077 r_free = 0.4077 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121189 restraints weight = 20478.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125173 restraints weight = 11418.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127730 restraints weight = 7215.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129590 restraints weight = 5020.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130830 restraints weight = 3748.372| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10395 Z= 0.154 Angle : 0.617 7.847 14128 Z= 0.320 Chirality : 0.042 0.208 1716 Planarity : 0.005 0.043 1757 Dihedral : 5.825 79.743 1458 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.81 % Allowed : 13.89 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.22), residues: 1319 helix: -0.62 (0.17), residues: 813 sheet: -2.92 (0.77), residues: 32 loop : -2.94 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 24 TYR 0.022 0.002 TYR A 556 PHE 0.017 0.001 PHE B 229 TRP 0.013 0.001 TRP B 83 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00324 (10395) covalent geometry : angle 0.61745 (14128) hydrogen bonds : bond 0.04491 ( 544) hydrogen bonds : angle 4.20272 ( 1593) *********************** 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 371 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.7268 (mmt90) REVERT: A 93 SER cc_start: 0.8447 (t) cc_final: 0.8060 (p) REVERT: A 122 PHE cc_start: 0.7287 (m-80) cc_final: 0.6824 (m-10) REVERT: A 123 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8475 (tp) cc_final: 0.7884 (tp) REVERT: A 199 ILE cc_start: 0.8167 (mt) cc_final: 0.7840 (mt) REVERT: A 231 VAL cc_start: 0.8728 (t) cc_final: 0.7994 (p) REVERT: A 235 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7748 (mm-40) REVERT: A 237 LYS cc_start: 0.8397 (ttpp) cc_final: 0.7982 (ttpp) REVERT: A 247 TYR cc_start: 0.7299 (m-10) cc_final: 0.6212 (m-10) REVERT: A 272 PHE cc_start: 0.7870 (t80) cc_final: 0.7326 (t80) REVERT: A 280 ILE cc_start: 0.8932 (mt) cc_final: 0.8703 (tp) REVERT: A 286 LYS cc_start: 0.9167 (tppt) cc_final: 0.8786 (mmmm) REVERT: A 355 SER cc_start: 0.7860 (m) cc_final: 0.7555 (p) REVERT: A 384 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5877 (mm-30) REVERT: A 395 SER cc_start: 0.8563 (m) cc_final: 0.8063 (p) REVERT: A 398 PHE cc_start: 0.7091 (m-80) cc_final: 0.6338 (m-10) REVERT: A 409 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7566 (ttp-170) REVERT: A 432 MET cc_start: 0.7287 (tpt) cc_final: 0.6655 (tpt) REVERT: A 473 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7934 (mtpt) REVERT: A 484 PHE cc_start: 0.8271 (t80) cc_final: 0.7890 (t80) REVERT: A 488 MET cc_start: 0.7407 (tpp) cc_final: 0.6974 (tpp) REVERT: A 512 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8340 (mtm-85) REVERT: A 530 TYR cc_start: 0.7160 (m-80) cc_final: 0.6932 (m-80) REVERT: A 546 LYS cc_start: 0.8250 (tptm) cc_final: 0.7778 (tptm) REVERT: A 549 ARG cc_start: 0.6989 (ttt90) cc_final: 0.6748 (ttm-80) REVERT: A 556 TYR cc_start: 0.8121 (p90) cc_final: 0.7691 (p90) REVERT: A 560 ASP cc_start: 0.8173 (m-30) cc_final: 0.7857 (t0) REVERT: A 563 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7941 (ttmm) REVERT: A 662 CYS cc_start: 0.7960 (m) cc_final: 0.7517 (m) REVERT: A 686 ILE cc_start: 0.8601 (pt) cc_final: 0.8316 (mm) REVERT: A 687 ASP cc_start: 0.6690 (t0) cc_final: 0.6251 (t0) REVERT: A 723 HIS cc_start: 0.7118 (t-170) cc_final: 0.6855 (t-90) REVERT: B 118 TYR cc_start: 0.7125 (m-10) cc_final: 0.6762 (m-80) REVERT: B 162 LEU cc_start: 0.4905 (tp) cc_final: 0.4704 (tp) REVERT: B 195 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6205 (tp) REVERT: B 199 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7501 (mp) REVERT: B 207 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 230 GLN cc_start: 0.7954 (tp40) cc_final: 0.7366 (tm-30) REVERT: B 231 VAL cc_start: 0.8664 (p) cc_final: 0.7895 (p) REVERT: B 235 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7253 (mm-40) REVERT: B 236 LEU cc_start: 0.8098 (tp) cc_final: 0.7721 (tp) REVERT: B 237 LYS cc_start: 0.8190 (pttt) cc_final: 0.7685 (pmtt) REVERT: B 251 LEU cc_start: 0.8319 (mm) cc_final: 0.6447 (mm) REVERT: B 255 TYR cc_start: 0.8234 (m-10) cc_final: 0.7683 (m-80) REVERT: B 259 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 263 ASN cc_start: 0.7308 (t0) cc_final: 0.6987 (t0) REVERT: B 271 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7561 (p0) REVERT: B 286 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7948 (ttmm) REVERT: B 293 LYS cc_start: 0.8560 (pptt) cc_final: 0.8270 (tppt) REVERT: B 309 ILE cc_start: 0.8846 (pt) cc_final: 0.8632 (mm) REVERT: B 320 GLU cc_start: 0.7569 (tp30) cc_final: 0.7238 (tp30) REVERT: B 359 VAL cc_start: 0.7795 (p) cc_final: 0.7528 (m) REVERT: B 395 SER cc_start: 0.7554 (m) cc_final: 0.7016 (p) REVERT: B 487 ILE cc_start: 0.8588 (pt) cc_final: 0.8215 (tp) REVERT: B 488 MET cc_start: 0.7138 (tpp) cc_final: 0.5945 (tpp) REVERT: B 492 LEU cc_start: 0.8534 (mt) cc_final: 0.7721 (mt) REVERT: B 499 LEU cc_start: 0.8270 (tp) cc_final: 0.8003 (tp) REVERT: B 560 ASP cc_start: 0.7979 (p0) cc_final: 0.7693 (p0) REVERT: B 583 LYS cc_start: 0.8769 (tmmt) cc_final: 0.8437 (tttm) REVERT: B 669 ASP cc_start: 0.7204 (p0) cc_final: 0.6994 (p0) REVERT: B 677 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7076 (ttp80) REVERT: B 686 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 701 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6955 (mm-30) REVERT: B 702 LYS cc_start: 0.7159 (tttm) cc_final: 0.6559 (tptm) REVERT: B 706 CYS cc_start: 0.7347 (m) cc_final: 0.6369 (m) outliers start: 54 outliers final: 31 residues processed: 349 average time/residue: 0.0960 time to fit residues: 46.2637 Evaluate side-chains 330 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 701 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL 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 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 246 ASN A 289 ASN A 383 GLN A 519 ASN A 567 ASN A 728 HIS B 324 ASN B 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.136588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.117456 restraints weight = 20700.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121365 restraints weight = 11572.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123964 restraints weight = 7272.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125760 restraints weight = 5021.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127013 restraints weight = 3728.469| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3305 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= 0.162 Angle : 0.622 8.229 14128 Z= 0.324 Chirality : 0.043 0.165 1716 Planarity : 0.004 0.053 1757 Dihedral : 5.719 81.554 1449 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.90 % Allowed : 17.01 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1319 helix: -0.06 (0.18), residues: 806 sheet: -2.53 (0.86), residues: 32 loop : -2.71 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.019 0.002 TYR A 556 PHE 0.016 0.001 PHE B 555 TRP 0.011 0.001 TRP B 83 HIS 0.007 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00347 (10395) covalent geometry : angle 0.62187 (14128) hydrogen bonds : bond 0.04191 ( 544) hydrogen bonds : angle 4.09512 ( 1593) *********************** 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 375 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.374 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: 0.7700 (mm110) cc_final: 0.7443 (mm110) REVERT: A 36 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7277 (mmt90) REVERT: A 37 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: A 93 SER cc_start: 0.8424 (t) cc_final: 0.8089 (p) REVERT: A 122 PHE cc_start: 0.7261 (m-80) cc_final: 0.6809 (m-10) REVERT: A 123 PRO cc_start: 0.8304 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8471 (tp) cc_final: 0.7895 (tp) REVERT: A 199 ILE cc_start: 0.8184 (mt) cc_final: 0.7850 (mt) REVERT: A 213 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7370 (mtm-85) REVERT: A 231 VAL cc_start: 0.8741 (t) cc_final: 0.8161 (p) REVERT: A 235 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7747 (mm-40) REVERT: A 237 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7955 (ttpp) REVERT: A 241 ASN cc_start: 0.8211 (t0) cc_final: 0.7932 (t0) REVERT: A 247 TYR cc_start: 0.7248 (m-10) cc_final: 0.6925 (m-10) REVERT: A 280 ILE cc_start: 0.8949 (mt) cc_final: 0.8700 (tp) REVERT: A 286 LYS cc_start: 0.9150 (tppt) cc_final: 0.8770 (mmmm) REVERT: A 355 SER cc_start: 0.7874 (m) cc_final: 0.7589 (p) REVERT: A 383 GLN cc_start: 0.7513 (mt0) cc_final: 0.7249 (mt0) REVERT: A 384 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5850 (mm-30) REVERT: A 392 ASN cc_start: 0.8357 (m-40) cc_final: 0.8152 (m110) REVERT: A 395 SER cc_start: 0.8432 (m) cc_final: 0.8055 (p) REVERT: A 398 PHE cc_start: 0.7056 (m-80) cc_final: 0.6451 (m-10) REVERT: A 409 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7535 (ttp-170) REVERT: A 432 MET cc_start: 0.7362 (tpt) cc_final: 0.7099 (tpt) REVERT: A 447 LYS cc_start: 0.8478 (mtpt) cc_final: 0.7976 (mttp) REVERT: A 457 ASN cc_start: 0.7945 (m110) cc_final: 0.7514 (m110) REVERT: A 473 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8014 (mtpt) REVERT: A 476 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8357 (mtpp) REVERT: A 478 ASP cc_start: 0.8305 (t0) cc_final: 0.7751 (t0) REVERT: A 484 PHE cc_start: 0.8286 (t80) cc_final: 0.7943 (t80) REVERT: A 488 MET cc_start: 0.7554 (tpp) cc_final: 0.7097 (tpp) REVERT: A 512 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7713 (mtm180) REVERT: A 530 TYR cc_start: 0.7329 (m-80) cc_final: 0.7091 (m-80) REVERT: A 546 LYS cc_start: 0.8252 (tptm) cc_final: 0.7734 (tptm) REVERT: A 549 ARG cc_start: 0.7142 (ttt90) cc_final: 0.6934 (ttm-80) REVERT: A 556 TYR cc_start: 0.8162 (p90) cc_final: 0.7842 (p90) REVERT: A 560 ASP cc_start: 0.8132 (m-30) cc_final: 0.7815 (t0) REVERT: A 563 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8106 (ttmm) REVERT: A 662 CYS cc_start: 0.8008 (m) cc_final: 0.7651 (m) REVERT: A 678 MET cc_start: 0.7179 (tmm) cc_final: 0.5864 (tmm) REVERT: A 686 ILE cc_start: 0.8644 (pt) cc_final: 0.8392 (mm) REVERT: A 687 ASP cc_start: 0.6746 (t0) cc_final: 0.6323 (t0) REVERT: A 698 ASP cc_start: 0.7637 (t0) cc_final: 0.7432 (t0) REVERT: A 715 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7096 (mmmm) REVERT: A 730 GLN cc_start: 0.8429 (mt0) cc_final: 0.8226 (mt0) REVERT: B 29 GLU cc_start: 0.6935 (mp0) cc_final: 0.6531 (mp0) REVERT: B 103 MET cc_start: 0.5794 (mmt) cc_final: 0.5575 (mmp) REVERT: B 118 TYR cc_start: 0.7143 (m-10) cc_final: 0.6880 (m-80) REVERT: B 195 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6246 (tp) REVERT: B 199 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 207 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 230 GLN cc_start: 0.7952 (tp40) cc_final: 0.7358 (tm-30) REVERT: B 231 VAL cc_start: 0.8642 (p) cc_final: 0.7879 (p) REVERT: B 235 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7298 (mm-40) REVERT: B 236 LEU cc_start: 0.8102 (tp) cc_final: 0.7739 (tp) REVERT: B 251 LEU cc_start: 0.8407 (mm) cc_final: 0.6550 (mm) REVERT: B 255 TYR cc_start: 0.8243 (m-10) cc_final: 0.7680 (m-80) REVERT: B 259 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 263 ASN cc_start: 0.7299 (t0) cc_final: 0.6954 (t0) REVERT: B 286 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7998 (ttmm) REVERT: B 293 LYS cc_start: 0.8572 (pptt) cc_final: 0.8270 (pptt) REVERT: B 309 ILE cc_start: 0.8869 (pt) cc_final: 0.8653 (mm) REVERT: B 320 GLU cc_start: 0.7670 (tp30) cc_final: 0.7354 (tp30) REVERT: B 395 SER cc_start: 0.7644 (m) cc_final: 0.7141 (p) REVERT: B 426 ILE cc_start: 0.8572 (mm) cc_final: 0.8354 (mm) REVERT: B 475 ASN cc_start: 0.7866 (t0) cc_final: 0.7495 (t0) REVERT: B 487 ILE cc_start: 0.8587 (pt) cc_final: 0.8325 (mt) REVERT: B 488 MET cc_start: 0.7142 (tpp) cc_final: 0.5836 (tpp) REVERT: B 492 LEU cc_start: 0.8620 (mt) cc_final: 0.7741 (mt) REVERT: B 499 LEU cc_start: 0.8269 (tp) cc_final: 0.7949 (tp) REVERT: B 502 LEU cc_start: 0.7907 (tp) cc_final: 0.7477 (tp) REVERT: B 677 ARG cc_start: 0.7537 (ttt180) cc_final: 0.7114 (ttp80) REVERT: B 701 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 702 LYS cc_start: 0.7174 (tttm) cc_final: 0.6286 (tptp) REVERT: B 706 CYS cc_start: 0.7281 (m) cc_final: 0.5863 (m) outliers start: 55 outliers final: 34 residues processed: 349 average time/residue: 0.1039 time to fit residues: 49.3639 Evaluate side-chains 337 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 ASN 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 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 681 LYS 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 5 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN A 519 ASN A 567 ASN A 732 GLN B 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117142 restraints weight = 20643.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121057 restraints weight = 11550.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123643 restraints weight = 7291.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125424 restraints weight = 5070.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126565 restraints weight = 3797.646| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3660 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= 0.141 Angle : 0.608 8.908 14128 Z= 0.316 Chirality : 0.042 0.196 1716 Planarity : 0.004 0.055 1757 Dihedral : 5.765 81.768 1449 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.54 % Allowed : 19.86 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1319 helix: 0.12 (0.18), residues: 822 sheet: -2.58 (0.87), residues: 34 loop : -2.69 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.025 0.002 TYR A 105 PHE 0.023 0.001 PHE A 130 TRP 0.011 0.001 TRP B 83 HIS 0.008 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00302 (10395) covalent geometry : angle 0.60778 (14128) hydrogen bonds : bond 0.03925 ( 544) hydrogen bonds : angle 4.01469 ( 1593) *********************** 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 334 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.7435 (mmt90) REVERT: A 37 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: A 79 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7346 (mmt90) REVERT: A 93 SER cc_start: 0.8463 (t) cc_final: 0.8098 (p) REVERT: A 105 TYR cc_start: 0.7534 (m-80) cc_final: 0.7290 (m-80) REVERT: A 122 PHE cc_start: 0.7267 (m-80) cc_final: 0.6826 (m-10) REVERT: A 123 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8448 (tp) cc_final: 0.7932 (tp) REVERT: A 199 ILE cc_start: 0.8199 (mt) cc_final: 0.7869 (mt) REVERT: A 231 VAL cc_start: 0.8780 (t) cc_final: 0.8162 (p) REVERT: A 235 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7755 (mm-40) REVERT: A 237 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8008 (ttpp) REVERT: A 279 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8773 (mm) REVERT: A 280 ILE cc_start: 0.8967 (mt) cc_final: 0.8741 (tp) REVERT: A 286 LYS cc_start: 0.9140 (tppt) cc_final: 0.8789 (mmmm) REVERT: A 355 SER cc_start: 0.7884 (m) cc_final: 0.7583 (p) REVERT: A 384 GLU cc_start: 0.6634 (mm-30) cc_final: 0.5857 (mm-30) REVERT: A 395 SER cc_start: 0.8428 (m) cc_final: 0.8073 (p) REVERT: A 398 PHE cc_start: 0.7054 (m-80) cc_final: 0.6550 (m-10) REVERT: A 432 MET cc_start: 0.7349 (tpt) cc_final: 0.7000 (tpt) REVERT: A 447 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7937 (mttp) REVERT: A 457 ASN cc_start: 0.8033 (m110) cc_final: 0.7517 (m110) REVERT: A 473 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8055 (mtpt) REVERT: A 478 ASP cc_start: 0.8211 (t0) cc_final: 0.7669 (t0) REVERT: A 484 PHE cc_start: 0.8235 (t80) cc_final: 0.7894 (t80) REVERT: A 488 MET cc_start: 0.7544 (tpp) cc_final: 0.7113 (tpp) REVERT: A 530 TYR cc_start: 0.7322 (m-80) cc_final: 0.7065 (m-80) REVERT: A 546 LYS cc_start: 0.8271 (tptm) cc_final: 0.7750 (tptm) REVERT: A 556 TYR cc_start: 0.8210 (p90) cc_final: 0.7912 (p90) REVERT: A 560 ASP cc_start: 0.8109 (m-30) cc_final: 0.7783 (t0) REVERT: A 563 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8024 (ttmm) REVERT: A 662 CYS cc_start: 0.7960 (m) cc_final: 0.7635 (m) REVERT: A 686 ILE cc_start: 0.8665 (pt) cc_final: 0.8411 (mm) REVERT: A 687 ASP cc_start: 0.6758 (t0) cc_final: 0.6330 (t0) REVERT: A 715 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7098 (mmmm) REVERT: B 103 MET cc_start: 0.5757 (mmt) cc_final: 0.5513 (mmp) REVERT: B 118 TYR cc_start: 0.7134 (m-10) cc_final: 0.6911 (m-80) REVERT: B 134 ARG cc_start: 0.6454 (mtt90) cc_final: 0.6240 (mtt90) REVERT: B 158 ASP cc_start: 0.5311 (m-30) cc_final: 0.4529 (m-30) REVERT: B 185 ARG cc_start: 0.6845 (mmt180) cc_final: 0.6016 (mmt90) REVERT: B 195 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6315 (tp) REVERT: B 199 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 207 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 230 GLN cc_start: 0.7897 (tp40) cc_final: 0.7301 (tm-30) REVERT: B 231 VAL cc_start: 0.8648 (p) cc_final: 0.7859 (p) REVERT: B 235 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7281 (mm-40) REVERT: B 236 LEU cc_start: 0.8078 (tp) cc_final: 0.7686 (tp) REVERT: B 237 LYS cc_start: 0.8245 (pttt) cc_final: 0.7821 (pttt) REVERT: B 251 LEU cc_start: 0.8399 (mm) cc_final: 0.6444 (mm) REVERT: B 255 TYR cc_start: 0.8212 (m-10) cc_final: 0.7684 (m-80) REVERT: B 259 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 263 ASN cc_start: 0.7412 (t0) cc_final: 0.6955 (t0) REVERT: B 293 LYS cc_start: 0.8592 (pptt) cc_final: 0.8192 (mmmm) REVERT: B 320 GLU cc_start: 0.7621 (tp30) cc_final: 0.7321 (tp30) REVERT: B 324 ASN cc_start: 0.7645 (t0) cc_final: 0.7321 (t0) REVERT: B 395 SER cc_start: 0.7714 (m) cc_final: 0.7209 (p) REVERT: B 473 LYS cc_start: 0.7902 (mttp) cc_final: 0.7255 (mtpp) REVERT: B 475 ASN cc_start: 0.7930 (t0) cc_final: 0.7595 (t0) REVERT: B 487 ILE cc_start: 0.8575 (pt) cc_final: 0.8369 (mt) REVERT: B 488 MET cc_start: 0.7122 (tpp) cc_final: 0.5787 (tpp) REVERT: B 492 LEU cc_start: 0.8628 (mt) cc_final: 0.7729 (mt) REVERT: B 499 LEU cc_start: 0.8306 (tp) cc_final: 0.8032 (tp) REVERT: B 502 LEU cc_start: 0.7956 (tp) cc_final: 0.7646 (mt) REVERT: B 677 ARG cc_start: 0.7513 (ttt180) cc_final: 0.7095 (ttp80) REVERT: B 687 ASP cc_start: 0.6739 (t0) cc_final: 0.6347 (t0) outliers start: 51 outliers final: 33 residues processed: 313 average time/residue: 0.0951 time to fit residues: 41.2581 Evaluate side-chains 322 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 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 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 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 53 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 446 GLN ** B 579 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.132268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.113200 restraints weight = 20797.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117015 restraints weight = 11737.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.119541 restraints weight = 7424.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121327 restraints weight = 5159.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.122440 restraints weight = 3853.235| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4194 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= 0.188 Angle : 0.650 8.213 14128 Z= 0.341 Chirality : 0.044 0.204 1716 Planarity : 0.005 0.057 1757 Dihedral : 6.022 86.116 1449 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.25 % Allowed : 19.41 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1319 helix: 0.16 (0.18), residues: 834 sheet: -2.52 (0.89), residues: 34 loop : -2.63 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.015 0.002 TYR A 556 PHE 0.019 0.001 PHE B 572 TRP 0.013 0.001 TRP B 83 HIS 0.005 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00388 (10395) covalent geometry : angle 0.65015 (14128) hydrogen bonds : bond 0.03992 ( 544) hydrogen bonds : angle 4.09911 ( 1593) *********************** 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 372 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7616 (mmt90) REVERT: A 37 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: A 93 SER cc_start: 0.8492 (t) cc_final: 0.8118 (p) REVERT: A 100 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7370 (mm) REVERT: A 101 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7198 (mm-40) REVERT: A 103 MET cc_start: 0.6954 (mtm) cc_final: 0.6740 (mtp) REVERT: A 105 TYR cc_start: 0.7618 (m-80) cc_final: 0.7365 (m-80) REVERT: A 122 PHE cc_start: 0.7298 (m-80) cc_final: 0.6847 (m-10) REVERT: A 123 PRO cc_start: 0.8332 (Cg_exo) cc_final: 0.8100 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8560 (tp) cc_final: 0.8073 (tp) REVERT: A 199 ILE cc_start: 0.8222 (mt) cc_final: 0.7876 (mt) REVERT: A 229 PHE cc_start: 0.8396 (t80) cc_final: 0.8182 (m-80) REVERT: A 231 VAL cc_start: 0.8823 (t) cc_final: 0.8174 (p) REVERT: A 234 SER cc_start: 0.8791 (m) cc_final: 0.8340 (t) REVERT: A 235 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7755 (mm-40) REVERT: A 237 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8167 (ttpp) REVERT: A 279 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8836 (mm) REVERT: A 286 LYS cc_start: 0.9129 (tppt) cc_final: 0.8734 (mmmm) REVERT: A 307 THR cc_start: 0.8507 (m) cc_final: 0.8198 (p) REVERT: A 384 GLU cc_start: 0.6720 (mm-30) cc_final: 0.5897 (mm-30) REVERT: A 395 SER cc_start: 0.8437 (m) cc_final: 0.8077 (p) REVERT: A 398 PHE cc_start: 0.7069 (m-80) cc_final: 0.6520 (m-80) REVERT: A 447 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7988 (mttp) REVERT: A 467 ASP cc_start: 0.7514 (m-30) cc_final: 0.7239 (p0) REVERT: A 473 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8147 (mtpt) REVERT: A 478 ASP cc_start: 0.8193 (t0) cc_final: 0.7635 (t0) REVERT: A 484 PHE cc_start: 0.8265 (t80) cc_final: 0.7929 (t80) REVERT: A 488 MET cc_start: 0.7621 (tpp) cc_final: 0.7104 (tpp) REVERT: A 512 ARG cc_start: 0.8529 (mtm180) cc_final: 0.7349 (mtm180) REVERT: A 537 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7963 (mmtt) REVERT: A 546 LYS cc_start: 0.8213 (tptm) cc_final: 0.7696 (tptm) REVERT: A 560 ASP cc_start: 0.8108 (m-30) cc_final: 0.7893 (t0) REVERT: A 662 CYS cc_start: 0.7962 (m) cc_final: 0.7656 (m) REVERT: A 686 ILE cc_start: 0.8736 (pt) cc_final: 0.8420 (mm) REVERT: A 687 ASP cc_start: 0.6974 (t0) cc_final: 0.6514 (t0) REVERT: A 698 ASP cc_start: 0.7632 (t0) cc_final: 0.7407 (t0) REVERT: A 715 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7225 (mmmm) REVERT: A 716 ASP cc_start: 0.7268 (t0) cc_final: 0.6900 (t0) REVERT: A 723 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: A 727 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6258 (mm) REVERT: A 730 GLN cc_start: 0.8561 (mt0) cc_final: 0.8351 (mt0) REVERT: A 732 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7105 (mm-40) REVERT: B 29 GLU cc_start: 0.7056 (mp0) cc_final: 0.6816 (mp0) REVERT: B 39 ARG cc_start: 0.6325 (ttm170) cc_final: 0.5773 (mtp180) REVERT: B 68 LEU cc_start: 0.8409 (mm) cc_final: 0.8123 (mt) REVERT: B 118 TYR cc_start: 0.7211 (m-10) cc_final: 0.6995 (m-80) REVERT: B 134 ARG cc_start: 0.6424 (mtt90) cc_final: 0.6211 (mtt90) REVERT: B 158 ASP cc_start: 0.5585 (m-30) cc_final: 0.4945 (m-30) REVERT: B 185 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6282 (mmt90) REVERT: B 195 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6307 (tp) REVERT: B 199 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 207 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 230 GLN cc_start: 0.7907 (tp40) cc_final: 0.7347 (tm-30) REVERT: B 231 VAL cc_start: 0.8651 (p) cc_final: 0.8176 (p) REVERT: B 235 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7489 (mm-40) REVERT: B 236 LEU cc_start: 0.8034 (tp) cc_final: 0.7616 (tp) REVERT: B 237 LYS cc_start: 0.8295 (pttt) cc_final: 0.7564 (pttp) REVERT: B 251 LEU cc_start: 0.8488 (mm) cc_final: 0.6634 (mm) REVERT: B 255 TYR cc_start: 0.8232 (m-10) cc_final: 0.7696 (m-80) REVERT: B 259 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 263 ASN cc_start: 0.7434 (t0) cc_final: 0.6917 (t0) REVERT: B 271 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7443 (p0) REVERT: B 293 LYS cc_start: 0.8613 (pptt) cc_final: 0.8346 (pptt) REVERT: B 320 GLU cc_start: 0.7655 (tp30) cc_final: 0.7382 (tp30) REVERT: B 340 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6824 (pp) REVERT: B 395 SER cc_start: 0.7900 (m) cc_final: 0.7342 (p) REVERT: B 487 ILE cc_start: 0.8643 (pt) cc_final: 0.8410 (mt) REVERT: B 488 MET cc_start: 0.7163 (tpp) cc_final: 0.5820 (tpp) REVERT: B 492 LEU cc_start: 0.8687 (mt) cc_final: 0.7761 (mt) REVERT: B 499 LEU cc_start: 0.8330 (tp) cc_final: 0.8017 (tp) REVERT: B 526 SER cc_start: 0.8516 (m) cc_final: 0.8274 (p) REVERT: B 537 LYS cc_start: 0.6853 (tppt) cc_final: 0.5851 (tptp) REVERT: B 556 TYR cc_start: 0.8348 (p90) cc_final: 0.8126 (p90) REVERT: B 677 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7115 (ttp80) REVERT: B 687 ASP cc_start: 0.6862 (t0) cc_final: 0.6487 (t0) REVERT: B 720 LEU cc_start: 0.8512 (mp) cc_final: 0.8207 (mp) REVERT: B 724 ASP cc_start: 0.7219 (m-30) cc_final: 0.6904 (m-30) outliers start: 59 outliers final: 35 residues processed: 347 average time/residue: 0.0998 time to fit residues: 47.0051 Evaluate side-chains 339 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 727 LEU 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 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 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 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 475 ASN ** B 579 ASN ** 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 = 0.3986 r_free = 0.3986 target = 0.133550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114574 restraints weight = 20664.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118386 restraints weight = 11651.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120889 restraints weight = 7377.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122617 restraints weight = 5110.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123897 restraints weight = 3826.262| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10395 Z= 0.148 Angle : 0.634 9.589 14128 Z= 0.328 Chirality : 0.043 0.222 1716 Planarity : 0.004 0.052 1757 Dihedral : 5.546 53.041 1446 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.52 % Allowed : 21.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1319 helix: 0.28 (0.18), residues: 822 sheet: -2.70 (0.97), residues: 28 loop : -2.53 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.032 0.002 TYR A 556 PHE 0.017 0.001 PHE B 572 TRP 0.012 0.001 TRP B 83 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00318 (10395) covalent geometry : angle 0.63413 (14128) hydrogen bonds : bond 0.03894 ( 544) hydrogen bonds : angle 4.04514 ( 1593) *********************** 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 367 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.339 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: 0.7913 (tpp-160) cc_final: 0.7624 (mmt90) REVERT: A 37 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6493 (pm20) REVERT: A 79 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7321 (mmt90) REVERT: A 93 SER cc_start: 0.8451 (t) cc_final: 0.8104 (p) REVERT: A 100 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7367 (mm) REVERT: A 103 MET cc_start: 0.6969 (mtm) cc_final: 0.6762 (mtp) REVERT: A 122 PHE cc_start: 0.7182 (m-80) cc_final: 0.6645 (m-10) REVERT: A 123 PRO cc_start: 0.8220 (Cg_exo) cc_final: 0.7914 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8535 (tp) cc_final: 0.8014 (tp) REVERT: A 199 ILE cc_start: 0.8193 (mt) cc_final: 0.7861 (mt) REVERT: A 229 PHE cc_start: 0.8391 (t80) cc_final: 0.8185 (m-80) REVERT: A 231 VAL cc_start: 0.8808 (t) cc_final: 0.8120 (p) REVERT: A 234 SER cc_start: 0.8798 (m) cc_final: 0.8278 (t) REVERT: A 235 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7715 (mm-40) REVERT: A 237 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8166 (ttpp) REVERT: A 259 GLU cc_start: 0.8158 (tt0) cc_final: 0.7935 (tm-30) REVERT: A 280 ILE cc_start: 0.8971 (mt) cc_final: 0.8753 (tp) REVERT: A 286 LYS cc_start: 0.9120 (tppt) cc_final: 0.8724 (mmmm) REVERT: A 304 VAL cc_start: 0.9024 (t) cc_final: 0.8699 (p) REVERT: A 306 VAL cc_start: 0.8972 (p) cc_final: 0.8761 (m) REVERT: A 335 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 383 GLN cc_start: 0.7354 (mt0) cc_final: 0.6838 (mp10) REVERT: A 384 GLU cc_start: 0.6684 (mm-30) cc_final: 0.5852 (mm-30) REVERT: A 395 SER cc_start: 0.8412 (m) cc_final: 0.8049 (p) REVERT: A 398 PHE cc_start: 0.6999 (m-80) cc_final: 0.6436 (m-80) REVERT: A 447 LYS cc_start: 0.8462 (mtpt) cc_final: 0.7914 (mttp) REVERT: A 457 ASN cc_start: 0.8138 (m110) cc_final: 0.7714 (m-40) REVERT: A 473 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8146 (mtpt) REVERT: A 478 ASP cc_start: 0.8086 (t0) cc_final: 0.7647 (t0) REVERT: A 484 PHE cc_start: 0.8214 (t80) cc_final: 0.7907 (t80) REVERT: A 488 MET cc_start: 0.7526 (tpp) cc_final: 0.7041 (tpp) REVERT: A 511 LEU cc_start: 0.8841 (mt) cc_final: 0.8588 (mm) REVERT: A 512 ARG cc_start: 0.8528 (mtm180) cc_final: 0.7288 (mtm180) REVERT: A 546 LYS cc_start: 0.8240 (tptm) cc_final: 0.7686 (tptm) REVERT: A 662 CYS cc_start: 0.7832 (m) cc_final: 0.7503 (m) REVERT: A 686 ILE cc_start: 0.8741 (pt) cc_final: 0.8433 (mm) REVERT: A 687 ASP cc_start: 0.6890 (t0) cc_final: 0.6437 (t0) REVERT: A 710 ASP cc_start: 0.7378 (p0) cc_final: 0.7058 (p0) REVERT: A 715 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7149 (mmmm) REVERT: A 716 ASP cc_start: 0.7243 (t0) cc_final: 0.6926 (t0) REVERT: A 723 HIS cc_start: 0.7286 (t70) cc_final: 0.6925 (t70) REVERT: A 728 HIS cc_start: 0.7401 (t-90) cc_final: 0.6510 (t-90) REVERT: B 68 LEU cc_start: 0.8412 (mm) cc_final: 0.8071 (mt) REVERT: B 134 ARG cc_start: 0.6490 (mtt90) cc_final: 0.6287 (mtt90) REVERT: B 158 ASP cc_start: 0.5535 (m-30) cc_final: 0.5279 (m-30) REVERT: B 192 LEU cc_start: 0.8584 (tp) cc_final: 0.8108 (pp) REVERT: B 195 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6285 (tp) REVERT: B 199 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 207 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 230 GLN cc_start: 0.7901 (tp40) cc_final: 0.7323 (tm-30) REVERT: B 231 VAL cc_start: 0.8639 (p) cc_final: 0.8166 (p) REVERT: B 235 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7461 (mm-40) REVERT: B 236 LEU cc_start: 0.7994 (tp) cc_final: 0.7589 (tp) REVERT: B 237 LYS cc_start: 0.8248 (pttt) cc_final: 0.7520 (pttp) REVERT: B 251 LEU cc_start: 0.8476 (mm) cc_final: 0.6580 (mm) REVERT: B 255 TYR cc_start: 0.8226 (m-10) cc_final: 0.7692 (m-80) REVERT: B 259 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 263 ASN cc_start: 0.7382 (t0) cc_final: 0.6781 (t0) REVERT: B 271 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 293 LYS cc_start: 0.8614 (pptt) cc_final: 0.8329 (pptt) REVERT: B 320 GLU cc_start: 0.7569 (tp30) cc_final: 0.7304 (tp30) REVERT: B 324 ASN cc_start: 0.7702 (t0) cc_final: 0.7414 (t0) REVERT: B 340 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6842 (pp) REVERT: B 395 SER cc_start: 0.7816 (m) cc_final: 0.7291 (p) REVERT: B 457 ASN cc_start: 0.7334 (m110) cc_final: 0.7098 (m-40) REVERT: B 475 ASN cc_start: 0.7905 (t0) cc_final: 0.7525 (t0) REVERT: B 487 ILE cc_start: 0.8622 (pt) cc_final: 0.8408 (mt) REVERT: B 488 MET cc_start: 0.7189 (tpp) cc_final: 0.5831 (tpp) REVERT: B 492 LEU cc_start: 0.8703 (mt) cc_final: 0.7764 (mt) REVERT: B 499 LEU cc_start: 0.8188 (tp) cc_final: 0.7888 (tp) REVERT: B 526 SER cc_start: 0.8531 (m) cc_final: 0.8324 (p) REVERT: B 537 LYS cc_start: 0.6842 (tppt) cc_final: 0.6091 (tptp) REVERT: B 677 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7096 (ttp80) REVERT: B 687 ASP cc_start: 0.6866 (t0) cc_final: 0.6496 (t0) REVERT: B 724 ASP cc_start: 0.7274 (m-30) cc_final: 0.6947 (m-30) outliers start: 62 outliers final: 43 residues processed: 342 average time/residue: 0.1003 time to fit residues: 47.0703 Evaluate side-chains 353 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 71 ILE 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 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 350 LEU Chi-restraints excluded: chain A residue 400 CYS 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 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 244 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 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.132218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.113215 restraints weight = 20581.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116967 restraints weight = 11608.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119452 restraints weight = 7385.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121186 restraints weight = 5149.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122261 restraints weight = 3861.669| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4569 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= 0.162 Angle : 0.661 9.504 14128 Z= 0.342 Chirality : 0.044 0.235 1716 Planarity : 0.004 0.052 1757 Dihedral : 5.495 52.770 1444 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.34 % Allowed : 22.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1319 helix: 0.33 (0.18), residues: 812 sheet: -2.74 (0.97), residues: 28 loop : -2.48 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.029 0.002 TYR A 105 PHE 0.017 0.001 PHE A 385 TRP 0.014 0.002 TRP A 83 HIS 0.015 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00348 (10395) covalent geometry : angle 0.66071 (14128) hydrogen bonds : bond 0.03937 ( 544) hydrogen bonds : angle 4.11622 ( 1593) *********************** 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 370 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 310 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7637 (mmt90) REVERT: A 37 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: A 79 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7388 (mmt90) REVERT: A 93 SER cc_start: 0.8447 (t) cc_final: 0.8126 (p) REVERT: A 122 PHE cc_start: 0.7148 (m-80) cc_final: 0.6676 (m-10) REVERT: A 123 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.7980 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8560 (tp) cc_final: 0.8061 (tp) REVERT: A 199 ILE cc_start: 0.8202 (mt) cc_final: 0.7865 (mt) REVERT: A 231 VAL cc_start: 0.8753 (t) cc_final: 0.8089 (p) REVERT: A 234 SER cc_start: 0.8799 (m) cc_final: 0.8202 (t) REVERT: A 235 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7645 (mm-40) REVERT: A 237 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8159 (ttpp) REVERT: A 259 GLU cc_start: 0.8153 (tt0) cc_final: 0.7891 (tm-30) REVERT: A 279 ILE cc_start: 0.9085 (mm) cc_final: 0.8853 (mm) REVERT: A 286 LYS cc_start: 0.9118 (tppt) cc_final: 0.8727 (mmmm) REVERT: A 304 VAL cc_start: 0.9016 (t) cc_final: 0.8577 (p) REVERT: A 307 THR cc_start: 0.8448 (m) cc_final: 0.8165 (p) REVERT: A 335 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 383 GLN cc_start: 0.7142 (mt0) cc_final: 0.6813 (mp10) REVERT: A 395 SER cc_start: 0.8444 (m) cc_final: 0.8084 (p) REVERT: A 398 PHE cc_start: 0.6978 (m-80) cc_final: 0.6452 (m-80) REVERT: A 447 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7868 (mttp) REVERT: A 457 ASN cc_start: 0.8116 (m110) cc_final: 0.7697 (m-40) REVERT: A 473 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8134 (mtpt) REVERT: A 476 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8271 (mmmm) REVERT: A 478 ASP cc_start: 0.7971 (t0) cc_final: 0.7561 (t0) REVERT: A 484 PHE cc_start: 0.8186 (t80) cc_final: 0.7903 (t80) REVERT: A 488 MET cc_start: 0.7453 (tpp) cc_final: 0.6965 (tpp) REVERT: A 511 LEU cc_start: 0.8906 (mt) cc_final: 0.8661 (mm) REVERT: A 512 ARG cc_start: 0.8472 (mtm180) cc_final: 0.7271 (mtm180) REVERT: A 546 LYS cc_start: 0.8222 (tptm) cc_final: 0.7700 (tptm) REVERT: A 662 CYS cc_start: 0.7857 (m) cc_final: 0.7531 (m) REVERT: A 681 LYS cc_start: 0.8087 (tptt) cc_final: 0.7688 (tptt) REVERT: A 682 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 686 ILE cc_start: 0.8745 (pt) cc_final: 0.7772 (mm) REVERT: A 705 GLN cc_start: 0.8037 (pt0) cc_final: 0.7815 (tt0) REVERT: A 710 ASP cc_start: 0.7397 (p0) cc_final: 0.7053 (p0) REVERT: A 715 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7167 (mmmm) REVERT: A 716 ASP cc_start: 0.7263 (t0) cc_final: 0.6919 (t0) REVERT: A 723 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6996 (t-90) REVERT: B 68 LEU cc_start: 0.8405 (mm) cc_final: 0.8035 (mt) REVERT: B 158 ASP cc_start: 0.5479 (m-30) cc_final: 0.5222 (m-30) REVERT: B 192 LEU cc_start: 0.8578 (tp) cc_final: 0.8117 (pp) REVERT: B 196 VAL cc_start: 0.8405 (t) cc_final: 0.8193 (m) REVERT: B 207 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 230 GLN cc_start: 0.7836 (tp40) cc_final: 0.7308 (tm-30) REVERT: B 231 VAL cc_start: 0.8635 (p) cc_final: 0.8161 (p) REVERT: B 235 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7430 (mm-40) REVERT: B 236 LEU cc_start: 0.8039 (tp) cc_final: 0.7621 (tp) REVERT: B 237 LYS cc_start: 0.8203 (pttt) cc_final: 0.7498 (pttp) REVERT: B 251 LEU cc_start: 0.8450 (mm) cc_final: 0.6597 (mm) REVERT: B 255 TYR cc_start: 0.8144 (m-10) cc_final: 0.7670 (m-80) REVERT: B 259 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 263 ASN cc_start: 0.7252 (t0) cc_final: 0.6692 (t0) REVERT: B 271 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7385 (p0) REVERT: B 293 LYS cc_start: 0.8613 (pptt) cc_final: 0.8335 (pptt) REVERT: B 320 GLU cc_start: 0.7482 (tp30) cc_final: 0.7241 (tp30) REVERT: B 324 ASN cc_start: 0.7812 (t0) cc_final: 0.7522 (t0) REVERT: B 395 SER cc_start: 0.8053 (m) cc_final: 0.7536 (p) REVERT: B 457 ASN cc_start: 0.7277 (m110) cc_final: 0.7044 (m-40) REVERT: B 459 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7596 (mmtt) REVERT: B 475 ASN cc_start: 0.7953 (t0) cc_final: 0.7629 (t0) REVERT: B 487 ILE cc_start: 0.8638 (pt) cc_final: 0.8380 (mm) REVERT: B 488 MET cc_start: 0.7062 (tpp) cc_final: 0.5777 (tpp) REVERT: B 492 LEU cc_start: 0.8688 (mt) cc_final: 0.7735 (mt) REVERT: B 499 LEU cc_start: 0.8227 (tp) cc_final: 0.7925 (tp) REVERT: B 537 LYS cc_start: 0.6873 (tppt) cc_final: 0.6411 (tptp) REVERT: B 677 ARG cc_start: 0.7432 (ttt180) cc_final: 0.7088 (ttp80) REVERT: B 687 ASP cc_start: 0.6827 (t0) cc_final: 0.6445 (t0) REVERT: B 699 VAL cc_start: 0.6430 (OUTLIER) cc_final: 0.6068 (t) REVERT: B 724 ASP cc_start: 0.7233 (m-30) cc_final: 0.6938 (m-30) outliers start: 60 outliers final: 44 residues processed: 350 average time/residue: 0.0987 time to fit residues: 47.8967 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 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 253 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 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 704 GLU Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 244 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 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.133198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.113947 restraints weight = 20599.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117745 restraints weight = 11666.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120301 restraints weight = 7425.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121995 restraints weight = 5165.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123243 restraints weight = 3900.981| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10395 Z= 0.147 Angle : 0.697 10.101 14128 Z= 0.360 Chirality : 0.044 0.290 1716 Planarity : 0.005 0.055 1757 Dihedral : 5.436 52.675 1442 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 4.81 % Allowed : 23.33 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1319 helix: 0.34 (0.18), residues: 813 sheet: -2.62 (0.98), residues: 28 loop : -2.42 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 586 TYR 0.026 0.002 TYR A 556 PHE 0.027 0.001 PHE A 210 TRP 0.014 0.002 TRP A 83 HIS 0.023 0.002 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00328 (10395) covalent geometry : angle 0.69695 (14128) hydrogen bonds : bond 0.04022 ( 544) hydrogen bonds : angle 4.15443 ( 1593) *********************** 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 360 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7860 (tpp-160) cc_final: 0.7624 (mmt90) REVERT: A 37 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: A 79 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7410 (mmt90) REVERT: A 93 SER cc_start: 0.8469 (t) cc_final: 0.8137 (p) REVERT: A 122 PHE cc_start: 0.7103 (m-80) cc_final: 0.6637 (m-10) REVERT: A 123 PRO cc_start: 0.8206 (Cg_exo) cc_final: 0.7933 (Cg_endo) REVERT: A 145 SER cc_start: 0.8061 (m) cc_final: 0.7676 (p) REVERT: A 195 LEU cc_start: 0.8519 (tp) cc_final: 0.8013 (tp) REVERT: A 199 ILE cc_start: 0.8151 (mt) cc_final: 0.7813 (mt) REVERT: A 231 VAL cc_start: 0.8736 (t) cc_final: 0.8035 (p) REVERT: A 235 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7726 (mm-40) REVERT: A 237 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8155 (ttpp) REVERT: A 259 GLU cc_start: 0.8152 (tt0) cc_final: 0.7851 (tm-30) REVERT: A 279 ILE cc_start: 0.9058 (mm) cc_final: 0.8803 (mm) REVERT: A 286 LYS cc_start: 0.9114 (tppt) cc_final: 0.8722 (mmmm) REVERT: A 304 VAL cc_start: 0.9010 (t) cc_final: 0.8734 (p) REVERT: A 306 VAL cc_start: 0.8969 (p) cc_final: 0.8760 (m) REVERT: A 335 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 395 SER cc_start: 0.8418 (m) cc_final: 0.8069 (p) REVERT: A 447 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7854 (mttp) REVERT: A 457 ASN cc_start: 0.8114 (m110) cc_final: 0.7684 (m-40) REVERT: A 473 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8059 (mtpt) REVERT: A 476 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8333 (mmmm) REVERT: A 478 ASP cc_start: 0.7938 (t0) cc_final: 0.7522 (t0) REVERT: A 484 PHE cc_start: 0.8157 (t80) cc_final: 0.7851 (t80) REVERT: A 488 MET cc_start: 0.7406 (tpp) cc_final: 0.6929 (tpp) REVERT: A 511 LEU cc_start: 0.8895 (mt) cc_final: 0.8657 (mm) REVERT: A 512 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7266 (mtm180) REVERT: A 537 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7564 (mttm) REVERT: A 546 LYS cc_start: 0.8251 (tptm) cc_final: 0.7690 (tptm) REVERT: A 552 SER cc_start: 0.7787 (m) cc_final: 0.7411 (p) REVERT: A 662 CYS cc_start: 0.7838 (m) cc_final: 0.7582 (m) REVERT: A 681 LYS cc_start: 0.8074 (tptt) cc_final: 0.7672 (tptt) REVERT: A 705 GLN cc_start: 0.8010 (pt0) cc_final: 0.7808 (tt0) REVERT: A 715 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7134 (mmmm) REVERT: A 716 ASP cc_start: 0.7234 (t0) cc_final: 0.6910 (t0) REVERT: A 723 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6765 (t-90) REVERT: B 68 LEU cc_start: 0.8366 (mm) cc_final: 0.7999 (mt) REVERT: B 134 ARG cc_start: 0.6355 (mtt90) cc_final: 0.6067 (mtt90) REVERT: B 158 ASP cc_start: 0.5443 (m-30) cc_final: 0.5183 (m-30) REVERT: B 192 LEU cc_start: 0.8572 (tp) cc_final: 0.8205 (pp) REVERT: B 207 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 230 GLN cc_start: 0.7837 (tp40) cc_final: 0.7312 (tm-30) REVERT: B 231 VAL cc_start: 0.8627 (p) cc_final: 0.8164 (p) REVERT: B 235 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7406 (mm-40) REVERT: B 236 LEU cc_start: 0.8056 (tp) cc_final: 0.7626 (tp) REVERT: B 237 LYS cc_start: 0.8184 (pttt) cc_final: 0.7472 (pttp) REVERT: B 251 LEU cc_start: 0.8437 (mm) cc_final: 0.6619 (mm) REVERT: B 255 TYR cc_start: 0.8141 (m-10) cc_final: 0.7680 (m-80) REVERT: B 259 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 263 ASN cc_start: 0.7255 (t0) cc_final: 0.6748 (t0) REVERT: B 271 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7404 (p0) REVERT: B 320 GLU cc_start: 0.7542 (tp30) cc_final: 0.7286 (tp30) REVERT: B 324 ASN cc_start: 0.7879 (t0) cc_final: 0.7566 (t0) REVERT: B 340 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6900 (pp) REVERT: B 395 SER cc_start: 0.7988 (m) cc_final: 0.7513 (p) REVERT: B 457 ASN cc_start: 0.7268 (m110) cc_final: 0.7036 (m-40) REVERT: B 459 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7601 (mmtt) REVERT: B 475 ASN cc_start: 0.7943 (t0) cc_final: 0.7651 (t0) REVERT: B 487 ILE cc_start: 0.8612 (pt) cc_final: 0.8375 (mm) REVERT: B 488 MET cc_start: 0.6985 (tpp) cc_final: 0.5703 (tpp) REVERT: B 492 LEU cc_start: 0.8590 (mt) cc_final: 0.7314 (mt) REVERT: B 499 LEU cc_start: 0.8218 (tp) cc_final: 0.7924 (tp) REVERT: B 537 LYS cc_start: 0.6908 (tppt) cc_final: 0.6251 (tptp) REVERT: B 677 ARG cc_start: 0.7437 (ttt180) cc_final: 0.7098 (ttp80) REVERT: B 687 ASP cc_start: 0.6804 (t0) cc_final: 0.6420 (t0) REVERT: B 724 ASP cc_start: 0.7252 (m-30) cc_final: 0.6976 (m-30) outliers start: 54 outliers final: 41 residues processed: 343 average time/residue: 0.1020 time to fit residues: 47.7539 Evaluate side-chains 343 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 202 VAL 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 461 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 723 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 244 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 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 0.0010 chunk 99 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.132164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112719 restraints weight = 20607.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.116589 restraints weight = 11632.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119143 restraints weight = 7394.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120925 restraints weight = 5167.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122202 restraints weight = 3873.411| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10395 Z= 0.162 Angle : 0.701 9.150 14128 Z= 0.362 Chirality : 0.045 0.396 1716 Planarity : 0.005 0.052 1757 Dihedral : 5.523 52.497 1442 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 4.54 % Allowed : 23.42 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1319 helix: 0.31 (0.18), residues: 803 sheet: -2.60 (0.99), residues: 28 loop : -2.45 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 213 TYR 0.025 0.002 TYR A 556 PHE 0.026 0.001 PHE A 210 TRP 0.015 0.002 TRP B 472 HIS 0.014 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00355 (10395) covalent geometry : angle 0.70139 (14128) hydrogen bonds : bond 0.03954 ( 544) hydrogen bonds : angle 4.19442 ( 1593) *********************** 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 368 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7599 (mm110) cc_final: 0.7386 (mm110) REVERT: A 36 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7691 (mmt90) REVERT: A 37 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6467 (pm20) REVERT: A 79 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7537 (mmt90) REVERT: A 93 SER cc_start: 0.8496 (t) cc_final: 0.8132 (p) REVERT: A 101 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7063 (mm-40) REVERT: A 122 PHE cc_start: 0.7116 (m-80) cc_final: 0.6636 (m-10) REVERT: A 123 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7859 (Cg_endo) REVERT: A 145 SER cc_start: 0.8101 (m) cc_final: 0.7760 (p) REVERT: A 195 LEU cc_start: 0.8546 (tp) cc_final: 0.8076 (tp) REVERT: A 199 ILE cc_start: 0.8137 (mt) cc_final: 0.7798 (mt) REVERT: A 231 VAL cc_start: 0.8796 (t) cc_final: 0.8105 (p) REVERT: A 234 SER cc_start: 0.8742 (m) cc_final: 0.8160 (t) REVERT: A 235 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7760 (mm-40) REVERT: A 237 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8229 (ttpp) REVERT: A 269 ILE cc_start: 0.7903 (pt) cc_final: 0.7535 (mp) REVERT: A 276 LEU cc_start: 0.8514 (mm) cc_final: 0.8129 (mt) REVERT: A 279 ILE cc_start: 0.9032 (mm) cc_final: 0.8367 (mm) REVERT: A 283 MET cc_start: 0.7888 (tpp) cc_final: 0.7555 (mpp) REVERT: A 286 LYS cc_start: 0.9123 (tppt) cc_final: 0.8752 (mmmm) REVERT: A 304 VAL cc_start: 0.9050 (t) cc_final: 0.8764 (p) REVERT: A 306 VAL cc_start: 0.8966 (p) cc_final: 0.8745 (m) REVERT: A 320 GLU cc_start: 0.6752 (tp30) cc_final: 0.6362 (tp30) REVERT: A 335 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 377 TYR cc_start: 0.7174 (p90) cc_final: 0.6865 (p90) REVERT: A 385 PHE cc_start: 0.8273 (t80) cc_final: 0.8042 (t80) REVERT: A 395 SER cc_start: 0.8453 (m) cc_final: 0.8076 (p) REVERT: A 413 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7190 (mm-40) REVERT: A 438 LEU cc_start: 0.8019 (tp) cc_final: 0.7796 (tp) REVERT: A 447 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7896 (mttp) REVERT: A 457 ASN cc_start: 0.8204 (m110) cc_final: 0.7757 (m-40) REVERT: A 464 GLN cc_start: 0.8623 (mt0) cc_final: 0.8174 (mt0) REVERT: A 473 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8130 (mtpt) REVERT: A 476 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8311 (mmmm) REVERT: A 478 ASP cc_start: 0.8067 (t0) cc_final: 0.7635 (t0) REVERT: A 484 PHE cc_start: 0.8251 (t80) cc_final: 0.7892 (t80) REVERT: A 488 MET cc_start: 0.7586 (tpp) cc_final: 0.7053 (tpp) REVERT: A 511 LEU cc_start: 0.8736 (mt) cc_final: 0.8480 (mm) REVERT: A 537 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7675 (mttp) REVERT: A 546 LYS cc_start: 0.8259 (tptm) cc_final: 0.7678 (tptm) REVERT: A 552 SER cc_start: 0.7737 (m) cc_final: 0.7285 (p) REVERT: A 662 CYS cc_start: 0.7984 (m) cc_final: 0.7712 (m) REVERT: A 667 PHE cc_start: 0.7869 (p90) cc_final: 0.7533 (p90) REVERT: A 681 LYS cc_start: 0.8135 (tptt) cc_final: 0.7710 (tptt) REVERT: A 705 GLN cc_start: 0.8010 (pt0) cc_final: 0.7782 (tt0) REVERT: A 715 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7071 (mmmm) REVERT: A 716 ASP cc_start: 0.7344 (t0) cc_final: 0.7009 (t0) REVERT: A 724 ASP cc_start: 0.6722 (m-30) cc_final: 0.6238 (m-30) REVERT: B 68 LEU cc_start: 0.8421 (mm) cc_final: 0.8059 (mt) REVERT: B 134 ARG cc_start: 0.6391 (mtt90) cc_final: 0.6100 (mtt90) REVERT: B 158 ASP cc_start: 0.5590 (m-30) cc_final: 0.5356 (m-30) REVERT: B 192 LEU cc_start: 0.8614 (tp) cc_final: 0.8246 (pp) REVERT: B 207 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 230 GLN cc_start: 0.7916 (tp40) cc_final: 0.7376 (tm-30) REVERT: B 231 VAL cc_start: 0.8623 (p) cc_final: 0.8150 (p) REVERT: B 235 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 236 LEU cc_start: 0.8024 (tp) cc_final: 0.7607 (tp) REVERT: B 237 LYS cc_start: 0.8272 (pttt) cc_final: 0.7532 (pttp) REVERT: B 251 LEU cc_start: 0.8448 (mm) cc_final: 0.6614 (mm) REVERT: B 255 TYR cc_start: 0.8223 (m-10) cc_final: 0.7704 (m-80) REVERT: B 259 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 263 ASN cc_start: 0.7347 (t0) cc_final: 0.6773 (t0) REVERT: B 271 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7501 (p0) REVERT: B 293 LYS cc_start: 0.8644 (pptt) cc_final: 0.8359 (pptt) REVERT: B 320 GLU cc_start: 0.7669 (tp30) cc_final: 0.7395 (tp30) REVERT: B 324 ASN cc_start: 0.7971 (t0) cc_final: 0.7679 (t0) REVERT: B 340 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6899 (pp) REVERT: B 395 SER cc_start: 0.7919 (m) cc_final: 0.7374 (p) REVERT: B 457 ASN cc_start: 0.7454 (m110) cc_final: 0.7179 (m-40) REVERT: B 459 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7567 (mmtt) REVERT: B 475 ASN cc_start: 0.7946 (t0) cc_final: 0.7663 (t0) REVERT: B 488 MET cc_start: 0.7130 (tpp) cc_final: 0.5824 (tpp) REVERT: B 492 LEU cc_start: 0.8687 (mt) cc_final: 0.7314 (mt) REVERT: B 499 LEU cc_start: 0.8195 (tp) cc_final: 0.7913 (tt) REVERT: B 503 LEU cc_start: 0.8114 (mm) cc_final: 0.7811 (mp) REVERT: B 537 LYS cc_start: 0.7046 (tppt) cc_final: 0.6708 (tptp) REVERT: B 677 ARG cc_start: 0.7518 (ttt180) cc_final: 0.7133 (ttp80) REVERT: B 687 ASP cc_start: 0.6935 (t0) cc_final: 0.6537 (t0) REVERT: B 694 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7302 (mp) REVERT: B 724 ASP cc_start: 0.7189 (m-30) cc_final: 0.6721 (t0) outliers start: 51 outliers final: 42 residues processed: 348 average time/residue: 0.1008 time to fit residues: 47.8609 Evaluate side-chains 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 300 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 400 CYS 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 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 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 244 THR 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 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 207 GLN ** B 579 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.131490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112375 restraints weight = 20423.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.116201 restraints weight = 11529.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118769 restraints weight = 7327.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120533 restraints weight = 5098.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121645 restraints weight = 3813.212| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5074 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= 0.177 Angle : 0.732 9.747 14128 Z= 0.379 Chirality : 0.046 0.366 1716 Planarity : 0.005 0.052 1757 Dihedral : 5.605 52.630 1442 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 4.19 % Allowed : 23.95 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1319 helix: 0.37 (0.19), residues: 795 sheet: -2.60 (1.00), residues: 28 loop : -2.36 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 213 TYR 0.030 0.002 TYR A 691 PHE 0.023 0.001 PHE A 210 TRP 0.015 0.002 TRP A 83 HIS 0.019 0.002 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00386 (10395) covalent geometry : angle 0.73183 (14128) hydrogen bonds : bond 0.04053 ( 544) hydrogen bonds : angle 4.29598 ( 1593) ********************** 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 363 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7688 (mmt90) REVERT: A 37 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6487 (pm20) REVERT: A 79 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7540 (mmt90) REVERT: A 93 SER cc_start: 0.8512 (t) cc_final: 0.8159 (p) REVERT: A 113 VAL cc_start: 0.8055 (t) cc_final: 0.7452 (p) REVERT: A 122 PHE cc_start: 0.7120 (m-80) cc_final: 0.6634 (m-10) REVERT: A 123 PRO cc_start: 0.8127 (Cg_exo) cc_final: 0.7840 (Cg_endo) REVERT: A 145 SER cc_start: 0.8152 (m) cc_final: 0.7771 (p) REVERT: A 195 LEU cc_start: 0.8567 (tp) cc_final: 0.8108 (tp) REVERT: A 199 ILE cc_start: 0.8165 (mt) cc_final: 0.7841 (mt) REVERT: A 231 VAL cc_start: 0.8805 (t) cc_final: 0.8110 (p) REVERT: A 234 SER cc_start: 0.8742 (m) cc_final: 0.8167 (t) REVERT: A 235 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7778 (mm-40) REVERT: A 237 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8208 (ttpp) REVERT: A 241 ASN cc_start: 0.8250 (t0) cc_final: 0.7973 (t0) REVERT: A 269 ILE cc_start: 0.7919 (pt) cc_final: 0.7556 (mp) REVERT: A 276 LEU cc_start: 0.8502 (mm) cc_final: 0.8130 (mm) REVERT: A 279 ILE cc_start: 0.9033 (mm) cc_final: 0.8367 (mm) REVERT: A 283 MET cc_start: 0.7874 (tpp) cc_final: 0.7564 (mpp) REVERT: A 286 LYS cc_start: 0.9122 (tppt) cc_final: 0.8750 (mmmm) REVERT: A 335 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6825 (t80) REVERT: A 377 TYR cc_start: 0.7229 (p90) cc_final: 0.6826 (p90) REVERT: A 385 PHE cc_start: 0.8256 (t80) cc_final: 0.8040 (t80) REVERT: A 395 SER cc_start: 0.8446 (m) cc_final: 0.8078 (p) REVERT: A 438 LEU cc_start: 0.8016 (tp) cc_final: 0.7812 (tt) REVERT: A 447 LYS cc_start: 0.8463 (mtpt) cc_final: 0.7908 (mttp) REVERT: A 457 ASN cc_start: 0.8198 (m110) cc_final: 0.7747 (m110) REVERT: A 459 LYS cc_start: 0.8767 (tppp) cc_final: 0.8403 (tppp) REVERT: A 473 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8143 (mtpt) REVERT: A 476 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8331 (mmmm) REVERT: A 478 ASP cc_start: 0.8050 (t0) cc_final: 0.7641 (t0) REVERT: A 488 MET cc_start: 0.7579 (tpp) cc_final: 0.6983 (tpp) REVERT: A 512 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8275 (mtt90) REVERT: A 537 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7690 (mttp) REVERT: A 546 LYS cc_start: 0.8279 (tptm) cc_final: 0.7694 (tptm) REVERT: A 552 SER cc_start: 0.7731 (m) cc_final: 0.7265 (p) REVERT: A 568 SER cc_start: 0.8889 (m) cc_final: 0.8662 (p) REVERT: A 662 CYS cc_start: 0.7945 (m) cc_final: 0.7696 (m) REVERT: A 667 PHE cc_start: 0.7852 (p90) cc_final: 0.7533 (p90) REVERT: A 681 LYS cc_start: 0.8166 (tptt) cc_final: 0.7797 (tptt) REVERT: A 715 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7062 (mmmm) REVERT: A 716 ASP cc_start: 0.7352 (t0) cc_final: 0.6896 (t0) REVERT: A 723 HIS cc_start: 0.7352 (t-90) cc_final: 0.7025 (t-90) REVERT: B 68 LEU cc_start: 0.8439 (mm) cc_final: 0.8070 (mt) REVERT: B 134 ARG cc_start: 0.6404 (mtt90) cc_final: 0.6117 (mtt90) REVERT: B 158 ASP cc_start: 0.5771 (m-30) cc_final: 0.5542 (m-30) REVERT: B 192 LEU cc_start: 0.8613 (tp) cc_final: 0.8148 (pp) REVERT: B 207 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 230 GLN cc_start: 0.7916 (tp40) cc_final: 0.7373 (tm-30) REVERT: B 231 VAL cc_start: 0.8628 (p) cc_final: 0.8149 (p) REVERT: B 235 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7464 (mm-40) REVERT: B 236 LEU cc_start: 0.8040 (tp) cc_final: 0.7619 (tp) REVERT: B 237 LYS cc_start: 0.8275 (pttt) cc_final: 0.7545 (pttp) REVERT: B 251 LEU cc_start: 0.8419 (mm) cc_final: 0.6587 (mm) REVERT: B 255 TYR cc_start: 0.8220 (m-10) cc_final: 0.7713 (m-80) REVERT: B 259 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 263 ASN cc_start: 0.7349 (t0) cc_final: 0.6771 (t0) REVERT: B 271 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 293 LYS cc_start: 0.8630 (pptt) cc_final: 0.8356 (pptt) REVERT: B 320 GLU cc_start: 0.7728 (tp30) cc_final: 0.7465 (tp30) REVERT: B 324 ASN cc_start: 0.7993 (t0) cc_final: 0.7735 (t0) REVERT: B 340 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6916 (pp) REVERT: B 395 SER cc_start: 0.7980 (m) cc_final: 0.7384 (p) REVERT: B 457 ASN cc_start: 0.7421 (m110) cc_final: 0.7129 (m-40) REVERT: B 459 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7598 (mmtt) REVERT: B 488 MET cc_start: 0.7139 (tpp) cc_final: 0.5790 (tpp) REVERT: B 492 LEU cc_start: 0.8706 (mt) cc_final: 0.7297 (mt) REVERT: B 499 LEU cc_start: 0.8236 (tp) cc_final: 0.7963 (tt) REVERT: B 503 LEU cc_start: 0.8117 (mm) cc_final: 0.7818 (mp) REVERT: B 537 LYS cc_start: 0.7197 (tppt) cc_final: 0.6288 (tptp) REVERT: B 677 ARG cc_start: 0.7499 (ttt180) cc_final: 0.7133 (ttp80) REVERT: B 687 ASP cc_start: 0.6946 (t0) cc_final: 0.6544 (t0) REVERT: B 724 ASP cc_start: 0.7197 (m-30) cc_final: 0.6757 (t0) outliers start: 47 outliers final: 42 residues processed: 346 average time/residue: 0.1001 time to fit residues: 47.7846 Evaluate side-chains 350 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 300 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 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 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 244 THR 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 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 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS A 322 ASN B 475 ASN ** B 579 ASN ** 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 = 0.3954 r_free = 0.3954 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.112305 restraints weight = 20682.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.116200 restraints weight = 11619.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118761 restraints weight = 7360.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120553 restraints weight = 5100.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121793 restraints weight = 3798.927| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 10395 Z= 0.292 Angle : 0.987 59.190 14128 Z= 0.556 Chirality : 0.047 0.395 1716 Planarity : 0.005 0.053 1757 Dihedral : 5.536 52.635 1440 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 4.54 % Allowed : 24.67 % Favored : 70.79 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1319 helix: 0.37 (0.19), residues: 795 sheet: -2.60 (1.01), residues: 28 loop : -2.37 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 213 TYR 0.023 0.002 TYR A 556 PHE 0.024 0.001 PHE A 210 TRP 0.014 0.002 TRP B 83 HIS 0.015 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00656 (10395) covalent geometry : angle 0.98728 (14128) hydrogen bonds : bond 0.04088 ( 544) hydrogen bonds : angle 4.30871 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.42 seconds wall clock time: 32 minutes 27.85 seconds (1947.85 seconds total)