Starting phenix.real_space_refine on Sun Jul 5 15:39:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.map" model { file = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nk2_12429/07_2026/7nk2_12429.cif" } resolution = 4.84 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= 0.027 sd= 0.342 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: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 107 5.16 5 C 9311 2.51 5 N 2595 2.21 5 O 2872 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28776 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11704 Classifications: {'peptide': 735} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4075 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "F" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 727 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 3 Time building chain proxies: 5.12, per 1000 atoms: 0.18 Number of scatterers: 28776 At special positions: 0 Unit cell: (102, 134, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 23 15.00 O 2872 8.00 N 2595 7.00 C 9311 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 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: 3.09 Conformation dependent library (CDL) restraints added in 733.4 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.6% alpha, 14.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.792A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.432A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.637A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.634A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.973A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.588A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.509A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.595A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.035A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.331A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.236A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.518A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 792 1.23 - 1.43: 5751 1.43 - 1.63: 8555 1.63 - 1.83: 185 Bond restraints: 29124 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.523 -0.065 1.40e-02 5.10e+03 2.16e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.515 1.486 0.029 9.30e-03 1.16e+04 9.64e+00 bond pdb=" CD ARG F 38 " pdb=" NE ARG F 38 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.40e-02 5.10e+03 8.55e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.40e-02 5.10e+03 7.87e+00 ... (remaining 29119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52249 5.65 - 11.29: 14 11.29 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.23: 5 Bond angle restraints: 52269 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.77 28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.32 27.68 3.00e+00 1.11e-01 8.52e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.91 27.09 3.00e+00 1.11e-01 8.15e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.47 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.77 -26.87 3.20e+00 9.77e-02 7.05e+01 ... (remaining 52264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12522 17.92 - 35.84: 857 35.84 - 53.76: 235 53.76 - 71.68: 70 71.68 - 89.60: 11 Dihedral angle restraints: 13695 sinusoidal: 7646 harmonic: 6049 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 138.40 -15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 13692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2200 0.112 - 0.224: 60 0.224 - 0.336: 3 0.336 - 0.448: 2 0.448 - 0.560: 1 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2263 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 59 " 0.057 2.00e-02 2.50e+03 4.05e-02 3.28e+01 pdb=" CG TYR F 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR F 59 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 59 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 59 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR F 59 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 59 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 114 " -0.070 2.00e-02 2.50e+03 3.31e-02 2.74e+01 pdb=" CG TRP F 114 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP F 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP F 114 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 114 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 114 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 114 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP F 114 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 72 " -0.212 9.50e-02 1.11e+02 9.82e-02 1.28e+01 pdb=" NE ARG F 72 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG F 72 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG F 72 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 72 " -0.022 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56222 2.78 - 3.39: 80820 3.39 - 3.99: 105815 3.99 - 4.60: 165098 Nonbonded interactions: 409217 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.620 2.450 ... (remaining 409212 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.170 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: 0.190 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.060 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4276 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 : 0.004 0.065 15257 Z= 0.245 Angle : 0.732 26.871 20678 Z= 0.429 Chirality : 0.046 0.560 2266 Planarity : 0.005 0.098 2583 Dihedral : 13.610 89.602 5889 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.32 % Allowed : 0.38 % Favored : 99.31 % Cbeta Deviations : 0.12 % 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: -0.71 (0.19), residues: 1778 helix: 0.45 (0.19), residues: 786 sheet: -0.63 (0.37), residues: 180 loop : -1.32 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG F 72 TYR 0.073 0.002 TYR F 59 PHE 0.048 0.002 PHE A 446 TRP 0.070 0.002 TRP F 114 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.25 (15256) covalent geometry : angle 0.73006 / 0.43 (20676) SS BOND : bond 0.01865 / 0.89 ( 1) SS BOND : angle 5.63692 / 3.22 ( 2) hydrogen bonds : bond 0.14928 / 9.74 ( 729) hydrogen bonds : angle 5.88797 / 4.24 ( 2006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 463 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 182 MET cc_start: -0.8027 (mpp) cc_final: -0.8851 (mtt) REVERT: A 268 LEU cc_start: 0.7540 (mt) cc_final: 0.7326 (mp) REVERT: A 367 LYS cc_start: 0.7037 (mttp) cc_final: 0.6796 (tmtt) REVERT: A 437 HIS cc_start: 0.7692 (m90) cc_final: 0.5800 (m90) REVERT: A 453 CYS cc_start: 0.9115 (t) cc_final: 0.8914 (t) REVERT: A 489 CYS cc_start: 0.8461 (p) cc_final: 0.8249 (p) REVERT: A 644 SER cc_start: 0.8864 (m) cc_final: 0.8224 (t) REVERT: B 22 PHE cc_start: 0.6950 (m-80) cc_final: 0.5805 (m-80) REVERT: B 25 THR cc_start: 0.9254 (p) cc_final: 0.8983 (p) REVERT: B 28 PRO cc_start: 0.6716 (Cg_endo) cc_final: 0.6125 (Cg_exo) REVERT: B 43 VAL cc_start: 0.8472 (t) cc_final: 0.8256 (t) REVERT: B 92 MET cc_start: 0.7829 (mmm) cc_final: 0.6981 (mmm) REVERT: B 314 ASN cc_start: 0.8203 (t0) cc_final: 0.7679 (t0) REVERT: B 414 MET cc_start: 0.7615 (mmm) cc_final: 0.6993 (mmm) REVERT: B 485 ASN cc_start: 0.5524 (p0) cc_final: 0.4649 (p0) REVERT: B 493 THR cc_start: 0.8654 (m) cc_final: 0.8425 (p) REVERT: B 525 ILE cc_start: 0.9340 (mt) cc_final: 0.9007 (tp) REVERT: B 568 ILE cc_start: 0.8010 (mt) cc_final: 0.7786 (mt) REVERT: B 645 MET cc_start: 0.4828 (mpp) cc_final: 0.4503 (mtp) REVERT: B 721 ARG cc_start: 0.5446 (ttt-90) cc_final: 0.3436 (tpt170) REVERT: F 68 PHE cc_start: 0.7775 (m-10) cc_final: 0.6117 (m-10) outliers start: 5 outliers final: 1 residues processed: 467 average time/residue: 0.3114 time to fit residues: 209.3122 Evaluate side-chains 297 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS B 306 ASN B 312 ASN B 425 ASN B 605 HIS F 39 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.197485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158361 restraints weight = 117087.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.164979 restraints weight = 60312.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.168306 restraints weight = 35440.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.170246 restraints weight = 24950.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.171048 restraints weight = 20800.096| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15257 Z= 0.218 Angle : 0.666 27.631 20678 Z= 0.359 Chirality : 0.040 0.160 2266 Planarity : 0.005 0.056 2583 Dihedral : 6.840 65.750 2229 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % 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: -0.82 (0.19), residues: 1778 helix: 0.25 (0.18), residues: 801 sheet: -0.74 (0.35), residues: 197 loop : -1.27 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.013 0.002 TYR A 393 PHE 0.033 0.002 PHE F 47 TRP 0.021 0.002 TRP A 338 HIS 0.009 0.002 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (15256) covalent geometry : angle 0.66637 / 0.36 (20676) SS BOND : bond 0.01164 / 0.55 ( 1) SS BOND : angle 1.23025 / 0.65 ( 2) hydrogen bonds : bond 0.04953 / 3.21 ( 729) hydrogen bonds : angle 5.19412 / 3.69 ( 2006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.8955 (mt) cc_final: 0.8701 (mt) REVERT: A 367 LYS cc_start: 0.7187 (mttp) cc_final: 0.6808 (tttp) REVERT: A 370 LEU cc_start: 0.8547 (mt) cc_final: 0.8245 (mt) REVERT: A 410 GLU cc_start: 0.7641 (tt0) cc_final: 0.6905 (tt0) REVERT: A 477 MET cc_start: 0.7005 (ptp) cc_final: 0.6765 (ptp) REVERT: A 523 MET cc_start: 0.7706 (mtm) cc_final: 0.7472 (mtm) REVERT: A 580 GLU cc_start: 0.8803 (tt0) cc_final: 0.8569 (tt0) REVERT: A 581 MET cc_start: 0.9459 (mtp) cc_final: 0.8824 (ttm) REVERT: A 644 SER cc_start: 0.8660 (m) cc_final: 0.8364 (t) REVERT: A 682 ASP cc_start: 0.7760 (t0) cc_final: 0.7103 (t0) REVERT: A 697 ASP cc_start: 0.8603 (t0) cc_final: 0.7879 (m-30) REVERT: B 131 TRP cc_start: 0.6690 (p-90) cc_final: 0.6377 (p-90) REVERT: B 348 MET cc_start: 0.6676 (mmm) cc_final: 0.5111 (mmt) REVERT: B 373 LEU cc_start: 0.9374 (mt) cc_final: 0.9036 (mt) REVERT: B 414 MET cc_start: 0.8798 (mmm) cc_final: 0.7981 (mmm) REVERT: B 445 ASP cc_start: 0.5845 (t0) cc_final: 0.5445 (t0) REVERT: B 744 MET cc_start: 0.7506 (tpt) cc_final: 0.6977 (mmm) REVERT: C 20 LEU cc_start: 0.8702 (mt) cc_final: 0.8486 (mt) REVERT: C 90 MET cc_start: 0.3709 (ttp) cc_final: 0.2835 (tpp) REVERT: F 34 MET cc_start: 0.6250 (mmp) cc_final: 0.5854 (mmm) REVERT: F 83 MET cc_start: 0.8307 (mtt) cc_final: 0.7924 (mtm) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.2955 time to fit residues: 142.8278 Evaluate side-chains 258 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 425 ASN B 569 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.191366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152382 restraints weight = 118179.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157821 restraints weight = 59796.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.161457 restraints weight = 36653.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.163824 restraints weight = 25999.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.164823 restraints weight = 20927.155| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15257 Z= 0.178 Angle : 0.607 25.805 20678 Z= 0.324 Chirality : 0.039 0.143 2266 Planarity : 0.005 0.085 2583 Dihedral : 6.814 71.055 2229 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.74 (0.19), residues: 1778 helix: 0.41 (0.18), residues: 809 sheet: -0.82 (0.35), residues: 209 loop : -1.33 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 559 TYR 0.013 0.002 TYR C 118 PHE 0.029 0.002 PHE F 47 TRP 0.015 0.002 TRP A 338 HIS 0.009 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (15256) covalent geometry : angle 0.60676 / 0.32 (20676) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 1.49027 / 0.79 ( 2) hydrogen bonds : bond 0.04757 / 3.07 ( 729) hydrogen bonds : angle 4.96410 / 3.51 ( 2006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 249 MET cc_start: 0.7636 (ttm) cc_final: 0.7240 (ttm) REVERT: A 284 LEU cc_start: 0.8949 (mt) cc_final: 0.8590 (mt) REVERT: A 370 LEU cc_start: 0.9050 (mt) cc_final: 0.8826 (mt) REVERT: A 410 GLU cc_start: 0.7617 (tt0) cc_final: 0.7354 (tt0) REVERT: A 477 MET cc_start: 0.7521 (ptp) cc_final: 0.7118 (ptp) REVERT: A 581 MET cc_start: 0.9532 (mtp) cc_final: 0.9069 (ttm) REVERT: A 682 ASP cc_start: 0.8350 (t0) cc_final: 0.8002 (t0) REVERT: A 697 ASP cc_start: 0.9160 (t0) cc_final: 0.7956 (m-30) REVERT: B 22 PHE cc_start: 0.8112 (m-80) cc_final: 0.7731 (m-80) REVERT: B 25 THR cc_start: 0.8929 (p) cc_final: 0.8513 (p) REVERT: B 67 ASN cc_start: 0.8050 (t0) cc_final: 0.7198 (m-40) REVERT: B 92 MET cc_start: 0.8994 (mmm) cc_final: 0.8279 (mmm) REVERT: B 179 MET cc_start: 0.6929 (ttp) cc_final: 0.6068 (tmm) REVERT: B 246 MET cc_start: 0.8162 (pmm) cc_final: 0.7791 (pmm) REVERT: B 256 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8570 (tp30) REVERT: B 267 GLU cc_start: 0.8072 (tt0) cc_final: 0.7693 (mp0) REVERT: B 348 MET cc_start: 0.6441 (mmm) cc_final: 0.4977 (mmm) REVERT: B 402 SER cc_start: 0.8485 (p) cc_final: 0.7621 (t) REVERT: B 493 THR cc_start: 0.8893 (m) cc_final: 0.8647 (p) REVERT: B 525 ILE cc_start: 0.9332 (tt) cc_final: 0.9061 (tp) REVERT: B 645 MET cc_start: 0.1806 (mpp) cc_final: 0.1332 (mtp) REVERT: B 673 SER cc_start: 0.8564 (t) cc_final: 0.8259 (p) REVERT: B 718 MET cc_start: 0.8636 (mtp) cc_final: 0.8099 (mmm) REVERT: B 744 MET cc_start: 0.7537 (tpt) cc_final: 0.7066 (mmm) REVERT: C 90 MET cc_start: 0.3691 (ttp) cc_final: 0.2783 (tpp) REVERT: F 83 MET cc_start: 0.7653 (mtt) cc_final: 0.7268 (mtm) REVERT: F 90 ASP cc_start: 0.8164 (m-30) cc_final: 0.7820 (m-30) REVERT: F 120 VAL cc_start: 0.8156 (t) cc_final: 0.7812 (t) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2677 time to fit residues: 121.9933 Evaluate side-chains 252 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.183840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141833 restraints weight = 109808.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147087 restraints weight = 56050.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.150742 restraints weight = 34820.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.152879 restraints weight = 25250.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153740 restraints weight = 20748.911| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15257 Z= 0.179 Angle : 0.605 28.218 20678 Z= 0.323 Chirality : 0.038 0.147 2266 Planarity : 0.005 0.093 2583 Dihedral : 6.867 76.112 2229 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.19), residues: 1778 helix: 0.52 (0.18), residues: 806 sheet: -0.85 (0.35), residues: 206 loop : -1.43 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 124 TYR 0.024 0.002 TYR C 118 PHE 0.023 0.002 PHE F 47 TRP 0.010 0.002 TRP F 36 HIS 0.011 0.002 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (15256) covalent geometry : angle 0.60538 / 0.32 (20676) SS BOND : bond 0.00087 / 0.04 ( 1) SS BOND : angle 0.56327 / 0.30 ( 2) hydrogen bonds : bond 0.04485 / 2.91 ( 729) hydrogen bonds : angle 4.98380 / 3.51 ( 2006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 249 MET cc_start: 0.7612 (ttm) cc_final: 0.7360 (ttm) REVERT: A 477 MET cc_start: 0.7852 (ptp) cc_final: 0.7618 (ptp) REVERT: A 682 ASP cc_start: 0.8715 (t0) cc_final: 0.8390 (t0) REVERT: A 697 ASP cc_start: 0.9317 (t0) cc_final: 0.8348 (m-30) REVERT: B 22 PHE cc_start: 0.8120 (m-80) cc_final: 0.7772 (m-80) REVERT: B 25 THR cc_start: 0.8919 (p) cc_final: 0.8624 (p) REVERT: B 92 MET cc_start: 0.9067 (mmm) cc_final: 0.8469 (mmm) REVERT: B 225 ASN cc_start: 0.8784 (t0) cc_final: 0.8275 (t0) REVERT: B 232 GLU cc_start: 0.8786 (tt0) cc_final: 0.8400 (tm-30) REVERT: B 246 MET cc_start: 0.8156 (pmm) cc_final: 0.7715 (pmm) REVERT: B 256 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8574 (tp30) REVERT: B 402 SER cc_start: 0.8748 (p) cc_final: 0.8521 (t) REVERT: B 568 ILE cc_start: 0.8242 (mt) cc_final: 0.7993 (mt) REVERT: B 570 THR cc_start: 0.4911 (p) cc_final: 0.4550 (m) REVERT: B 645 MET cc_start: 0.1405 (mpp) cc_final: 0.0964 (mtp) REVERT: B 658 ASP cc_start: 0.7282 (m-30) cc_final: 0.7035 (m-30) REVERT: B 673 SER cc_start: 0.8739 (t) cc_final: 0.8335 (p) REVERT: B 744 MET cc_start: 0.7561 (tpt) cc_final: 0.7083 (mmm) REVERT: C 90 MET cc_start: 0.3367 (ttp) cc_final: 0.3021 (tpp) REVERT: F 83 MET cc_start: 0.8003 (mtt) cc_final: 0.7765 (mtm) REVERT: F 90 ASP cc_start: 0.8175 (m-30) cc_final: 0.7793 (m-30) REVERT: F 120 VAL cc_start: 0.8331 (t) cc_final: 0.8004 (t) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2536 time to fit residues: 114.9339 Evaluate side-chains 258 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 177 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS B 425 ASN B 476 ASN B 634 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140170 restraints weight = 119888.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145221 restraints weight = 61523.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148761 restraints weight = 39099.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.150893 restraints weight = 29250.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151669 restraints weight = 24621.386| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15257 Z= 0.148 Angle : 0.567 27.069 20678 Z= 0.299 Chirality : 0.038 0.215 2266 Planarity : 0.004 0.041 2583 Dihedral : 6.851 79.514 2229 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.06 % Allowed : 0.76 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.19), residues: 1778 helix: 0.70 (0.18), residues: 804 sheet: -0.81 (0.36), residues: 208 loop : -1.43 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.012 0.001 TYR F 59 PHE 0.016 0.001 PHE F 47 TRP 0.015 0.002 TRP B 437 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15256) covalent geometry : angle 0.56737 / 0.30 (20676) SS BOND : bond 0.01789 / 0.85 ( 1) SS BOND : angle 0.96008 / 0.52 ( 2) hydrogen bonds : bond 0.04318 / 2.80 ( 729) hydrogen bonds : angle 4.86825 / 3.44 ( 2006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 12 MET cc_start: 0.7572 (ppp) cc_final: 0.6901 (ppp) REVERT: A 249 MET cc_start: 0.7678 (ttm) cc_final: 0.7280 (ttm) REVERT: A 407 ILE cc_start: 0.7534 (tt) cc_final: 0.7322 (tt) REVERT: A 410 GLU cc_start: 0.8005 (tt0) cc_final: 0.7759 (tt0) REVERT: A 477 MET cc_start: 0.7923 (ptp) cc_final: 0.7722 (ptp) REVERT: A 676 LEU cc_start: 0.8287 (mt) cc_final: 0.7960 (mt) REVERT: A 682 ASP cc_start: 0.8819 (t0) cc_final: 0.8532 (t0) REVERT: A 697 ASP cc_start: 0.9364 (t0) cc_final: 0.8520 (m-30) REVERT: B 22 PHE cc_start: 0.8259 (m-80) cc_final: 0.7869 (m-80) REVERT: B 25 THR cc_start: 0.8886 (p) cc_final: 0.8554 (p) REVERT: B 78 GLU cc_start: 0.9341 (mp0) cc_final: 0.9089 (mp0) REVERT: B 92 MET cc_start: 0.9071 (mmm) cc_final: 0.8483 (mmm) REVERT: B 179 MET cc_start: 0.7032 (ttp) cc_final: 0.5631 (tmm) REVERT: B 225 ASN cc_start: 0.8656 (t0) cc_final: 0.8178 (t0) REVERT: B 232 GLU cc_start: 0.8706 (tt0) cc_final: 0.8442 (tm-30) REVERT: B 246 MET cc_start: 0.7900 (pmm) cc_final: 0.7590 (pmm) REVERT: B 267 GLU cc_start: 0.7877 (tt0) cc_final: 0.7605 (mp0) REVERT: B 289 MET cc_start: 0.6310 (mmt) cc_final: 0.6077 (mmt) REVERT: B 411 MET cc_start: 0.7887 (mpp) cc_final: 0.7478 (mmt) REVERT: B 414 MET cc_start: 0.8554 (mmm) cc_final: 0.8121 (mmm) REVERT: B 452 ASN cc_start: 0.8063 (m-40) cc_final: 0.7518 (t0) REVERT: B 459 ILE cc_start: 0.9376 (mm) cc_final: 0.9151 (mm) REVERT: B 568 ILE cc_start: 0.8256 (mt) cc_final: 0.8050 (mt) REVERT: B 570 THR cc_start: 0.4966 (p) cc_final: 0.4604 (m) REVERT: B 664 HIS cc_start: 0.6160 (m90) cc_final: 0.5843 (m-70) REVERT: B 673 SER cc_start: 0.8666 (t) cc_final: 0.8302 (p) REVERT: B 718 MET cc_start: 0.8458 (mtp) cc_final: 0.7797 (mmm) REVERT: B 744 MET cc_start: 0.7624 (tpt) cc_final: 0.7091 (mmm) REVERT: C 90 MET cc_start: 0.3894 (ttp) cc_final: 0.3418 (tpp) REVERT: F 83 MET cc_start: 0.8294 (mtt) cc_final: 0.8011 (mtt) REVERT: F 90 ASP cc_start: 0.8339 (m-30) cc_final: 0.7943 (m-30) REVERT: F 120 VAL cc_start: 0.8525 (t) cc_final: 0.8218 (t) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.2418 time to fit residues: 107.5163 Evaluate side-chains 254 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 89 optimal weight: 0.0980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.179195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134927 restraints weight = 111512.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140045 restraints weight = 56498.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143613 restraints weight = 35496.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145581 restraints weight = 26166.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.146489 restraints weight = 21899.537| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15257 Z= 0.156 Angle : 0.582 25.979 20678 Z= 0.307 Chirality : 0.038 0.165 2266 Planarity : 0.004 0.045 2583 Dihedral : 6.982 88.368 2229 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.49 (0.19), residues: 1778 helix: 0.84 (0.18), residues: 813 sheet: -0.66 (0.37), residues: 195 loop : -1.51 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.033 0.002 TYR B 30 PHE 0.022 0.002 PHE F 47 TRP 0.011 0.002 TRP B 437 HIS 0.011 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (15256) covalent geometry : angle 0.58213 / 0.31 (20676) SS BOND : bond 0.01761 / 0.84 ( 1) SS BOND : angle 1.31608 / 0.71 ( 2) hydrogen bonds : bond 0.04237 / 2.75 ( 729) hydrogen bonds : angle 4.81547 / 3.39 ( 2006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.7865 (ttm) cc_final: 0.7324 (ttm) REVERT: A 459 ILE cc_start: 0.9705 (mt) cc_final: 0.9504 (mm) REVERT: A 516 ASP cc_start: 0.8266 (m-30) cc_final: 0.7429 (t70) REVERT: A 597 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 667 LEU cc_start: 0.9601 (tp) cc_final: 0.8860 (tp) REVERT: A 682 ASP cc_start: 0.8962 (t0) cc_final: 0.7032 (p0) REVERT: A 697 ASP cc_start: 0.9381 (t0) cc_final: 0.8364 (m-30) REVERT: A 707 PHE cc_start: 0.9210 (t80) cc_final: 0.8863 (t80) REVERT: B 22 PHE cc_start: 0.8231 (m-80) cc_final: 0.7979 (m-80) REVERT: B 25 THR cc_start: 0.8829 (p) cc_final: 0.8557 (p) REVERT: B 90 GLU cc_start: 0.8695 (tt0) cc_final: 0.8345 (tt0) REVERT: B 92 MET cc_start: 0.9105 (mmm) cc_final: 0.8487 (mmm) REVERT: B 179 MET cc_start: 0.7175 (ttp) cc_final: 0.5588 (tmm) REVERT: B 225 ASN cc_start: 0.8698 (t0) cc_final: 0.8369 (t0) REVERT: B 232 GLU cc_start: 0.8786 (tt0) cc_final: 0.8505 (tm-30) REVERT: B 246 MET cc_start: 0.7911 (pmm) cc_final: 0.7585 (pmm) REVERT: B 256 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8517 (mm-30) REVERT: B 267 GLU cc_start: 0.7811 (tt0) cc_final: 0.6819 (tm-30) REVERT: B 289 MET cc_start: 0.6316 (mmt) cc_final: 0.6052 (mmt) REVERT: B 367 GLN cc_start: 0.7674 (mt0) cc_final: 0.7148 (pm20) REVERT: B 459 ILE cc_start: 0.9509 (mm) cc_final: 0.9290 (mm) REVERT: B 570 THR cc_start: 0.4438 (p) cc_final: 0.3909 (m) REVERT: B 664 HIS cc_start: 0.6572 (m90) cc_final: 0.5759 (m-70) REVERT: B 673 SER cc_start: 0.8698 (t) cc_final: 0.8329 (p) REVERT: B 744 MET cc_start: 0.7658 (tpt) cc_final: 0.7326 (mmp) REVERT: C 90 MET cc_start: 0.4082 (ttp) cc_final: 0.3540 (tpp) REVERT: F 120 VAL cc_start: 0.8784 (t) cc_final: 0.8583 (t) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2408 time to fit residues: 110.0232 Evaluate side-chains 254 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 408 GLN B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.175566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133809 restraints weight = 114539.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138850 restraints weight = 57457.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142204 restraints weight = 35711.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144166 restraints weight = 26175.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145078 restraints weight = 21802.914| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15257 Z= 0.162 Angle : 0.596 28.744 20678 Z= 0.311 Chirality : 0.038 0.158 2266 Planarity : 0.004 0.040 2583 Dihedral : 7.027 93.955 2229 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -0.51 (0.19), residues: 1778 helix: 0.82 (0.18), residues: 813 sheet: -0.63 (0.37), residues: 195 loop : -1.52 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.016 0.002 TYR B 599 PHE 0.026 0.002 PHE A 176 TRP 0.015 0.002 TRP F 36 HIS 0.009 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (15256) covalent geometry : angle 0.59558 / 0.31 (20676) SS BOND : bond 0.00614 / 0.29 ( 1) SS BOND : angle 1.45981 / 0.84 ( 2) hydrogen bonds : bond 0.04350 / 2.85 ( 729) hydrogen bonds : angle 4.95812 / 3.51 ( 2006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASP cc_start: 0.8475 (m-30) cc_final: 0.8019 (t70) REVERT: A 561 MET cc_start: 0.7002 (ttt) cc_final: 0.6784 (ttt) REVERT: A 581 MET cc_start: 0.9607 (mtp) cc_final: 0.8857 (tpp) REVERT: A 597 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 676 LEU cc_start: 0.8641 (mp) cc_final: 0.8142 (mp) REVERT: A 682 ASP cc_start: 0.8990 (t0) cc_final: 0.7197 (p0) REVERT: A 697 ASP cc_start: 0.9390 (t0) cc_final: 0.8197 (m-30) REVERT: B 22 PHE cc_start: 0.8275 (m-80) cc_final: 0.8026 (m-80) REVERT: B 25 THR cc_start: 0.8849 (p) cc_final: 0.8575 (p) REVERT: B 40 MET cc_start: 0.9099 (ptm) cc_final: 0.8888 (ptm) REVERT: B 92 MET cc_start: 0.9156 (mmm) cc_final: 0.8522 (mmm) REVERT: B 179 MET cc_start: 0.7199 (ttp) cc_final: 0.5629 (tmm) REVERT: B 225 ASN cc_start: 0.8666 (t0) cc_final: 0.8278 (t0) REVERT: B 246 MET cc_start: 0.7869 (pmm) cc_final: 0.7497 (pmm) REVERT: B 267 GLU cc_start: 0.7839 (tt0) cc_final: 0.6827 (tm-30) REVERT: B 331 GLU cc_start: 0.7097 (pm20) cc_final: 0.6356 (pp20) REVERT: B 348 MET cc_start: 0.6337 (mmm) cc_final: 0.5932 (mmm) REVERT: B 359 SER cc_start: 0.6685 (t) cc_final: 0.6259 (m) REVERT: B 459 ILE cc_start: 0.9561 (mm) cc_final: 0.9348 (mm) REVERT: B 673 SER cc_start: 0.8699 (t) cc_final: 0.8357 (p) REVERT: B 744 MET cc_start: 0.7642 (tpt) cc_final: 0.7309 (mmp) REVERT: C 90 MET cc_start: 0.3578 (ttp) cc_final: 0.3304 (tpp) REVERT: F 120 VAL cc_start: 0.8906 (t) cc_final: 0.8705 (t) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2487 time to fit residues: 108.3560 Evaluate side-chains 244 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 313 GLN B 413 ASN B 425 ASN B 569 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.168767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128089 restraints weight = 118179.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132423 restraints weight = 61630.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.135568 restraints weight = 39691.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137224 restraints weight = 29765.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138256 restraints weight = 25216.568| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.8038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 15257 Z= 0.260 Angle : 0.694 27.477 20678 Z= 0.378 Chirality : 0.041 0.227 2266 Planarity : 0.006 0.053 2583 Dihedral : 7.408 99.565 2229 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.06 % Allowed : 1.07 % Favored : 98.86 % 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: -1.19 (0.19), residues: 1778 helix: 0.22 (0.18), residues: 813 sheet: -0.81 (0.37), residues: 192 loop : -1.88 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 663 TYR 0.019 0.003 TYR B 82 PHE 0.032 0.002 PHE B 496 TRP 0.024 0.003 TRP F 36 HIS 0.010 0.002 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (15256) covalent geometry : angle 0.69409 / 0.38 (20676) SS BOND : bond 0.00218 / 0.10 ( 1) SS BOND : angle 2.33022 / 1.25 ( 2) hydrogen bonds : bond 0.05052 / 3.29 ( 729) hydrogen bonds : angle 5.49909 / 3.89 ( 2006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.8628 (t80) cc_final: 0.8023 (t80) REVERT: A 437 HIS cc_start: 0.8617 (t70) cc_final: 0.8295 (t70) REVERT: A 515 THR cc_start: 0.8339 (p) cc_final: 0.7509 (p) REVERT: A 676 LEU cc_start: 0.8807 (mp) cc_final: 0.8306 (mp) REVERT: A 682 ASP cc_start: 0.9031 (t0) cc_final: 0.8056 (p0) REVERT: A 697 ASP cc_start: 0.9484 (t0) cc_final: 0.8454 (m-30) REVERT: A 707 PHE cc_start: 0.9448 (t80) cc_final: 0.8926 (t80) REVERT: B 22 PHE cc_start: 0.8445 (m-80) cc_final: 0.8241 (m-80) REVERT: B 25 THR cc_start: 0.8984 (p) cc_final: 0.8561 (p) REVERT: B 69 ILE cc_start: 0.9296 (mm) cc_final: 0.9076 (tp) REVERT: B 78 GLU cc_start: 0.8882 (mp0) cc_final: 0.8619 (mp0) REVERT: B 172 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 225 ASN cc_start: 0.8838 (t0) cc_final: 0.8579 (t0) REVERT: B 246 MET cc_start: 0.8242 (pmm) cc_final: 0.7759 (pmm) REVERT: B 267 GLU cc_start: 0.8086 (tt0) cc_final: 0.7014 (tm-30) REVERT: B 289 MET cc_start: 0.6336 (mmt) cc_final: 0.5986 (mmt) REVERT: B 313 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: B 331 GLU cc_start: 0.6926 (pm20) cc_final: 0.6116 (pp20) REVERT: B 411 MET cc_start: 0.8114 (mpp) cc_final: 0.7824 (mmt) REVERT: B 452 ASN cc_start: 0.8094 (m-40) cc_final: 0.7700 (t0) REVERT: B 604 LEU cc_start: 0.8829 (tp) cc_final: 0.8578 (tp) REVERT: B 666 TRP cc_start: 0.6810 (p-90) cc_final: 0.6541 (p-90) REVERT: B 673 SER cc_start: 0.8597 (t) cc_final: 0.8339 (p) REVERT: B 744 MET cc_start: 0.7688 (tpt) cc_final: 0.7356 (mmp) REVERT: F 79 LEU cc_start: 0.7384 (tp) cc_final: 0.7080 (tp) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.2601 time to fit residues: 103.6440 Evaluate side-chains 237 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4320 r_free = 0.4320 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131933 restraints weight = 124034.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136385 restraints weight = 64701.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139723 restraints weight = 42205.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141456 restraints weight = 32166.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142632 restraints weight = 27607.914| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.8127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15257 Z= 0.113 Angle : 0.567 27.328 20678 Z= 0.296 Chirality : 0.038 0.162 2266 Planarity : 0.005 0.134 2583 Dihedral : 7.007 100.343 2229 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.19), residues: 1778 helix: 0.84 (0.18), residues: 816 sheet: -0.66 (0.37), residues: 190 loop : -1.59 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 468 TYR 0.013 0.001 TYR B 599 PHE 0.022 0.002 PHE B 699 TRP 0.016 0.002 TRP A 577 HIS 0.008 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15256) covalent geometry : angle 0.56743 / 0.30 (20676) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.70169 / 0.37 ( 2) hydrogen bonds : bond 0.04223 / 2.77 ( 729) hydrogen bonds : angle 4.78846 / 3.36 ( 2006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8190 (ptm160) REVERT: A 232 TYR cc_start: 0.8633 (t80) cc_final: 0.7981 (t80) REVERT: A 249 MET cc_start: 0.7941 (ttp) cc_final: 0.7309 (ptm) REVERT: A 282 PHE cc_start: 0.9162 (p90) cc_final: 0.8889 (p90) REVERT: A 286 ASP cc_start: 0.8246 (m-30) cc_final: 0.7732 (m-30) REVERT: A 410 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 437 HIS cc_start: 0.8506 (t70) cc_final: 0.8180 (m-70) REVERT: A 603 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8383 (ptpt) REVERT: A 676 LEU cc_start: 0.8769 (mp) cc_final: 0.8256 (mp) REVERT: A 686 LEU cc_start: 0.9259 (tp) cc_final: 0.9038 (mt) REVERT: A 697 ASP cc_start: 0.9410 (t0) cc_final: 0.8231 (m-30) REVERT: A 707 PHE cc_start: 0.9261 (t80) cc_final: 0.8530 (t80) REVERT: B 22 PHE cc_start: 0.8158 (m-80) cc_final: 0.7710 (m-80) REVERT: B 25 THR cc_start: 0.8574 (p) cc_final: 0.8263 (p) REVERT: B 106 SER cc_start: 0.8907 (m) cc_final: 0.8677 (t) REVERT: B 225 ASN cc_start: 0.8758 (t0) cc_final: 0.8410 (t0) REVERT: B 246 MET cc_start: 0.7736 (pmm) cc_final: 0.7384 (pmm) REVERT: B 256 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8777 (mm-30) REVERT: B 267 GLU cc_start: 0.7850 (tt0) cc_final: 0.7285 (tm-30) REVERT: B 331 GLU cc_start: 0.6784 (pm20) cc_final: 0.6151 (pp20) REVERT: B 348 MET cc_start: 0.6218 (mmm) cc_final: 0.5780 (mmm) REVERT: B 411 MET cc_start: 0.7966 (mpp) cc_final: 0.7753 (mmt) REVERT: B 452 ASN cc_start: 0.8214 (m-40) cc_final: 0.7669 (t0) REVERT: B 491 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6985 (mm-30) REVERT: B 507 MET cc_start: 0.4309 (mtm) cc_final: 0.3359 (tmm) REVERT: B 568 ILE cc_start: 0.8965 (mt) cc_final: 0.8282 (tt) REVERT: B 664 HIS cc_start: 0.7332 (m90) cc_final: 0.6769 (m-70) REVERT: B 673 SER cc_start: 0.8537 (t) cc_final: 0.8213 (p) REVERT: B 744 MET cc_start: 0.7706 (tpt) cc_final: 0.7367 (mmp) REVERT: C 11 MET cc_start: 0.8706 (mmt) cc_final: 0.7938 (mmm) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2289 time to fit residues: 96.1932 Evaluate side-chains 236 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 425 ASN B 569 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.173205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130879 restraints weight = 122472.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135461 restraints weight = 64213.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138618 restraints weight = 41533.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140599 restraints weight = 31421.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141411 restraints weight = 26506.509| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.8357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15257 Z= 0.125 Angle : 0.558 26.880 20678 Z= 0.291 Chirality : 0.037 0.146 2266 Planarity : 0.005 0.085 2583 Dihedral : 6.942 100.483 2229 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: -0.37 (0.20), residues: 1778 helix: 0.99 (0.18), residues: 816 sheet: -0.55 (0.37), residues: 195 loop : -1.53 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.020 0.001 TYR A 540 PHE 0.017 0.001 PHE B 496 TRP 0.023 0.001 TRP B 666 HIS 0.008 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (15256) covalent geometry : angle 0.55765 / 0.29 (20676) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.75922 / 0.40 ( 2) hydrogen bonds : bond 0.04108 / 2.70 ( 729) hydrogen bonds : angle 4.76820 / 3.33 ( 2006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 232 TYR cc_start: 0.8588 (t80) cc_final: 0.7881 (t80) REVERT: A 282 PHE cc_start: 0.9162 (p90) cc_final: 0.8915 (p90) REVERT: A 410 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 437 HIS cc_start: 0.8466 (t70) cc_final: 0.8179 (m-70) REVERT: A 523 MET cc_start: 0.8070 (mtm) cc_final: 0.7323 (mtm) REVERT: A 597 GLU cc_start: 0.8774 (pt0) cc_final: 0.8463 (pp20) REVERT: A 603 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8385 (ptpt) REVERT: A 676 LEU cc_start: 0.8760 (mp) cc_final: 0.8298 (mp) REVERT: A 686 LEU cc_start: 0.9259 (tp) cc_final: 0.9056 (mt) REVERT: A 697 ASP cc_start: 0.9403 (t0) cc_final: 0.8367 (m-30) REVERT: A 707 PHE cc_start: 0.9114 (t80) cc_final: 0.8470 (t80) REVERT: B 22 PHE cc_start: 0.8118 (m-80) cc_final: 0.7729 (m-80) REVERT: B 40 MET cc_start: 0.9650 (ptm) cc_final: 0.9442 (ptm) REVERT: B 225 ASN cc_start: 0.8794 (t0) cc_final: 0.8406 (t0) REVERT: B 246 MET cc_start: 0.7701 (pmm) cc_final: 0.7338 (pmm) REVERT: B 256 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8444 (mm-30) REVERT: B 267 GLU cc_start: 0.7807 (tt0) cc_final: 0.6609 (tm-30) REVERT: B 331 GLU cc_start: 0.6809 (pm20) cc_final: 0.6206 (pp20) REVERT: B 348 MET cc_start: 0.6378 (mmm) cc_final: 0.5927 (mmm) REVERT: B 452 ASN cc_start: 0.8273 (m-40) cc_final: 0.7729 (t0) REVERT: B 507 MET cc_start: 0.4438 (mtm) cc_final: 0.3466 (tmm) REVERT: B 568 ILE cc_start: 0.8996 (mt) cc_final: 0.8345 (tt) REVERT: B 673 SER cc_start: 0.8576 (t) cc_final: 0.8177 (p) REVERT: B 744 MET cc_start: 0.7696 (tpt) cc_final: 0.7357 (mmp) REVERT: C 11 MET cc_start: 0.8710 (mmt) cc_final: 0.7930 (mmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2289 time to fit residues: 93.9972 Evaluate side-chains 227 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 64 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 81 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 62 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 overall best weight: 0.9058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 425 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.172714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130698 restraints weight = 117216.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135555 restraints weight = 59346.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138984 restraints weight = 37390.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140838 restraints weight = 27509.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142068 restraints weight = 22963.441| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15257 Z= 0.110 Angle : 0.540 26.928 20678 Z= 0.281 Chirality : 0.037 0.159 2266 Planarity : 0.005 0.082 2583 Dihedral : 6.892 101.169 2229 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.20), residues: 1778 helix: 1.08 (0.18), residues: 826 sheet: -0.40 (0.38), residues: 183 loop : -1.46 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.019 0.001 TYR A 464 PHE 0.026 0.001 PHE B 496 TRP 0.021 0.001 TRP B 666 HIS 0.008 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15256) covalent geometry : angle 0.54046 / 0.28 (20676) SS BOND : bond 0.00010 / 0.00 ( 1) SS BOND : angle 0.54735 / 0.29 ( 2) hydrogen bonds : bond 0.03874 / 2.54 ( 729) hydrogen bonds : angle 4.62778 / 3.23 ( 2006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5454.96 seconds wall clock time: 93 minutes 50.50 seconds (5630.50 seconds total)