Starting phenix.real_space_refine on Sun Jul 5 15:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk1_12428/07_2026/7nk1_12428.map" } resolution = 4.22 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= 0.003 sd= 0.037 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 106 5.16 5 C 9289 2.51 5 N 2595 2.21 5 O 2866 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: 28747 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 3 Time building chain proxies: 4.64, per 1000 atoms: 0.16 Number of scatterers: 28747 At special positions: 0 Unit cell: (97.2, 103.68, 158.76, 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 106 16.00 P 23 15.00 O 2866 8.00 N 2595 7.00 C 9289 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 95 " 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: 2.81 Conformation dependent library (CDL) restraints added in 702.5 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 17 sheets defined 50.0% alpha, 13.8% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.89 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: 4.005A 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: 3.793A 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: 4.431A 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: 3.947A 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: 3.630A 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: 4.635A 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: 3.972A 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: 5.827A 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: 3.587A 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: 3.508A 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: 3.594A 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: 4.511A 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: 4.036A 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: 3.892A 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: 4.237A 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: 3.523A 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: 4.302A 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 60 through 64 removed outlier: 3.504A pdb=" N ARG F 64 " --> pdb=" O ASP F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A 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: 4.137A 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: 3.835A 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: 3.816A 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: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A 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: 6.035A 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: 11.690A 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: 6.065A 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: 6.929A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.164A 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: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A 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: 6.035A 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: 6.174A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A 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: 3.515A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A 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: 3.522A 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: 6.144A pdb=" N GLY F 10 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP F 96 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY F 35 " --> pdb=" O TRP F 96 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1974 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: 6.85 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 147 1.23 - 1.43: 6277 1.43 - 1.62: 8647 1.62 - 1.82: 183 Bond restraints: 29095 Sorted by residual: bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.510 1.472 0.039 1.20e-02 6.94e+03 1.03e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.84e+00 bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.40e-02 5.10e+03 8.21e+00 bond pdb=" N PRO F 14 " pdb=" CA PRO F 14 " ideal model delta sigma weight residual 1.467 1.432 0.035 1.21e-02 6.83e+03 8.15e+00 ... (remaining 29090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52225 5.65 - 11.29: 5 11.29 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.23: 5 Bond angle restraints: 52236 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 80.27 27.73 3.00e+00 1.11e-01 8.54e+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 81.82 27.18 3.00e+00 1.11e-01 8.21e+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 82.46 26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.68 -26.78 3.20e+00 9.77e-02 7.00e+01 ... (remaining 52231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12507 17.94 - 35.88: 851 35.88 - 53.81: 237 53.81 - 71.75: 69 71.75 - 89.69: 10 Dihedral angle restraints: 13674 sinusoidal: 7637 harmonic: 6037 Sorted by residual: 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 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 13671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2026 0.067 - 0.134: 214 0.134 - 0.201: 22 0.201 - 0.268: 2 0.268 - 0.335: 1 Chirality restraints: 2265 Sorted by residual: chirality pdb=" CA ASN F 76 " pdb=" N ASN F 76 " pdb=" C ASN F 76 " pdb=" CB ASN F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" C PRO F 41 " pdb=" CB PRO F 41 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN F 84 " pdb=" N ASN F 84 " pdb=" C ASN F 84 " pdb=" CB ASN F 84 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2262 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 96 " -0.132 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP F 96 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP F 96 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP F 96 " 0.088 2.00e-02 2.50e+03 pdb=" NE1 TRP F 96 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP F 96 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 96 " 0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 96 " -0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 96 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP F 96 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " 0.111 2.00e-02 2.50e+03 6.23e-02 7.77e+01 pdb=" CG TYR F 37 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 108 " -0.054 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP F 108 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP F 108 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP F 108 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP F 108 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP F 108 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 108 " 0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 108 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 108 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 108 " -0.039 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1256 2.17 - 2.78: 56190 2.78 - 3.39: 80855 3.39 - 3.99: 105792 3.99 - 4.60: 165058 Nonbonded interactions: 409151 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 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 409146 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1934 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 0.044 15228 Z= 0.223 Angle : 0.691 26.779 20645 Z= 0.401 Chirality : 0.043 0.335 2265 Planarity : 0.005 0.076 2579 Dihedral : 13.555 89.689 5876 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.19 % Allowed : 0.44 % Favored : 99.37 % 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: -0.71 (0.19), residues: 1775 helix: 0.46 (0.19), residues: 786 sheet: -0.79 (0.38), residues: 176 loop : -1.29 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 71 TYR 0.111 0.002 TYR F 37 PHE 0.048 0.002 PHE A 446 TRP 0.132 0.004 TRP F 96 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.22 (15227) covalent geometry : angle 0.68913 / 0.40 (20643) SS BOND : bond 0.02507 / 1.19 ( 1) SS BOND : angle 5.06722 / 2.80 ( 2) hydrogen bonds : bond 0.15070 / 9.86 ( 727) hydrogen bonds : angle 5.96927 / 4.29 ( 1994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 334 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.716 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 561 MET cc_start: -0.1278 (tmm) cc_final: -0.1730 (tmm) REVERT: B 290 MET cc_start: 0.4741 (tpt) cc_final: 0.2828 (tpp) REVERT: B 408 MET cc_start: 0.3890 (tpt) cc_final: 0.3211 (tpt) REVERT: B 611 LEU cc_start: 0.3481 (tp) cc_final: 0.3147 (tt) REVERT: C 87 ASP cc_start: 0.2216 (p0) cc_final: 0.1806 (m-30) outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.3155 time to fit residues: 148.3884 Evaluate side-chains 223 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 703 ASN B 134 ASN B 312 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 676 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5409 r_free = 0.5409 target = 0.264687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.243931 restraints weight = 108046.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.250192 restraints weight = 57780.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.254150 restraints weight = 33150.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.256795 restraints weight = 21362.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.258548 restraints weight = 14831.301| |-----------------------------------------------------------------------------| r_work (final): 0.5339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2940 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15228 Z= 0.164 Angle : 0.646 27.461 20645 Z= 0.338 Chirality : 0.039 0.167 2265 Planarity : 0.005 0.069 2579 Dihedral : 6.805 62.675 2226 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.28 % 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: -0.67 (0.19), residues: 1775 helix: 0.33 (0.19), residues: 778 sheet: -0.60 (0.39), residues: 186 loop : -1.12 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 706 TYR 0.023 0.002 TYR C 111 PHE 0.022 0.002 PHE A 46 TRP 0.013 0.002 TRP A 88 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15227) covalent geometry : angle 0.64598 / 0.34 (20643) SS BOND : bond 0.00318 / 0.15 ( 1) SS BOND : angle 0.46710 / 0.27 ( 2) hydrogen bonds : bond 0.04744 / 3.06 ( 727) hydrogen bonds : angle 5.09353 / 3.61 ( 1994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 249 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.528 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: A 477 MET cc_start: 0.6380 (mpp) cc_final: 0.6169 (mpp) REVERT: A 523 MET cc_start: -0.2143 (mpp) cc_final: -0.2474 (mpp) REVERT: B 141 THR cc_start: 0.5986 (m) cc_final: 0.5760 (m) REVERT: B 290 MET cc_start: 0.5152 (tpt) cc_final: 0.4699 (tpt) REVERT: B 372 MET cc_start: 0.2495 (ttm) cc_final: 0.2100 (ttm) REVERT: B 408 MET cc_start: 0.2646 (tpt) cc_final: 0.2436 (tpp) REVERT: B 507 MET cc_start: 0.6378 (mmp) cc_final: 0.6112 (mmp) REVERT: C 87 ASP cc_start: 0.4047 (p0) cc_final: 0.3109 (m-30) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.3071 time to fit residues: 108.1413 Evaluate side-chains 203 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.0010 chunk 58 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 GLN B 335 ASN B 425 ASN B 476 ASN B 537 ASN B 641 ASN B 756 GLN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.260382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.239371 restraints weight = 107467.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.245821 restraints weight = 56474.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.249751 restraints weight = 32728.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.252262 restraints weight = 21410.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.253762 restraints weight = 14994.275| |-----------------------------------------------------------------------------| r_work (final): 0.5301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3137 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15228 Z= 0.149 Angle : 0.588 25.682 20645 Z= 0.310 Chirality : 0.038 0.164 2265 Planarity : 0.005 0.072 2579 Dihedral : 6.743 67.640 2226 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1775 helix: 0.26 (0.18), residues: 806 sheet: -0.60 (0.37), residues: 207 loop : -1.19 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.022 0.002 TYR B 620 PHE 0.021 0.002 PHE C 119 TRP 0.017 0.001 TRP F 96 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15227) covalent geometry : angle 0.58769 / 0.31 (20643) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.83527 / 0.48 ( 2) hydrogen bonds : bond 0.04553 / 3.01 ( 727) hydrogen bonds : angle 4.92298 / 3.51 ( 1994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 236 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.013 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 79 ILE cc_start: 0.7920 (mm) cc_final: 0.7612 (mm) REVERT: A 477 MET cc_start: 0.6172 (mpp) cc_final: 0.5690 (mpp) REVERT: A 607 MET cc_start: 0.5030 (tpp) cc_final: 0.4805 (tpp) REVERT: B 356 MET cc_start: 0.4440 (tpp) cc_final: 0.3970 (tpp) REVERT: B 408 MET cc_start: 0.2851 (tpt) cc_final: 0.2170 (tpt) REVERT: B 507 MET cc_start: 0.6499 (mmp) cc_final: 0.5866 (mmp) REVERT: B 655 MET cc_start: 0.1348 (mmm) cc_final: 0.1012 (mmt) REVERT: C 53 MET cc_start: 0.3378 (mmt) cc_final: 0.3122 (mmt) REVERT: C 87 ASP cc_start: 0.4281 (p0) cc_final: 0.3309 (m-30) REVERT: F 64 ARG cc_start: 0.1393 (mmt180) cc_final: 0.1097 (mmt180) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2982 time to fit residues: 99.9220 Evaluate side-chains 207 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.255263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.231567 restraints weight = 111504.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.238079 restraints weight = 60388.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.242427 restraints weight = 36714.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.245208 restraints weight = 24667.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.247121 restraints weight = 17780.322| |-----------------------------------------------------------------------------| r_work (final): 0.5245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3379 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15228 Z= 0.170 Angle : 0.630 28.219 20645 Z= 0.334 Chirality : 0.039 0.158 2265 Planarity : 0.006 0.105 2579 Dihedral : 7.041 73.702 2226 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -0.75 (0.19), residues: 1775 helix: 0.18 (0.18), residues: 797 sheet: -0.35 (0.38), residues: 197 loop : -1.17 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 124 TYR 0.028 0.002 TYR B 30 PHE 0.018 0.002 PHE B 466 TRP 0.044 0.002 TRP A 422 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15227) covalent geometry : angle 0.62998 / 0.33 (20643) SS BOND : bond 0.00677 / 0.32 ( 1) SS BOND : angle 0.87453 / 0.46 ( 2) hydrogen bonds : bond 0.04491 / 2.96 ( 727) hydrogen bonds : angle 4.96021 / 3.52 ( 1994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 234 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.587 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: -0.3471 (mmp) cc_final: -0.3704 (mmp) REVERT: A 477 MET cc_start: 0.6439 (mpp) cc_final: 0.5665 (mpp) REVERT: A 591 GLN cc_start: 0.6916 (tp40) cc_final: 0.6679 (tp40) REVERT: B 290 MET cc_start: 0.1281 (tpt) cc_final: 0.0943 (tpt) REVERT: B 372 MET cc_start: 0.3038 (ttm) cc_final: 0.2763 (ttm) REVERT: B 408 MET cc_start: 0.3155 (tpt) cc_final: 0.2386 (tpt) REVERT: B 655 MET cc_start: 0.1831 (mmm) cc_final: 0.1544 (mmt) REVERT: C 87 ASP cc_start: 0.4607 (p0) cc_final: 0.3730 (m-30) REVERT: F 64 ARG cc_start: 0.1295 (mmt180) cc_final: 0.0913 (mmt180) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2899 time to fit residues: 96.1695 Evaluate side-chains 213 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 670 GLN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5327 r_free = 0.5327 target = 0.252653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.228099 restraints weight = 112593.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.234621 restraints weight = 60920.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.239133 restraints weight = 37361.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.241936 restraints weight = 25295.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.243659 restraints weight = 18484.312| |-----------------------------------------------------------------------------| r_work (final): 0.5211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3505 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15228 Z= 0.161 Angle : 0.595 25.810 20645 Z= 0.316 Chirality : 0.038 0.154 2265 Planarity : 0.005 0.079 2579 Dihedral : 7.189 77.898 2226 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.06 % Allowed : 1.96 % Favored : 97.98 % 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: -0.77 (0.19), residues: 1775 helix: 0.22 (0.18), residues: 796 sheet: -0.45 (0.37), residues: 201 loop : -1.23 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 663 TYR 0.019 0.002 TYR B 30 PHE 0.021 0.002 PHE A 503 TRP 0.016 0.002 TRP B 580 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15227) covalent geometry : angle 0.59472 / 0.32 (20643) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 1.25099 / 0.72 ( 2) hydrogen bonds : bond 0.04412 / 2.92 ( 727) hydrogen bonds : angle 4.95198 / 3.50 ( 1994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 236 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.832 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: A 182 MET cc_start: -0.3403 (mmp) cc_final: -0.3633 (mmp) REVERT: A 477 MET cc_start: 0.6486 (mpp) cc_final: 0.5959 (mpp) REVERT: B 372 MET cc_start: 0.3216 (ttm) cc_final: 0.2962 (ttm) REVERT: C 87 ASP cc_start: 0.4621 (p0) cc_final: 0.3914 (m-30) REVERT: F 64 ARG cc_start: 0.0794 (mmt180) cc_final: 0.0483 (mmt180) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.2808 time to fit residues: 93.1727 Evaluate side-chains 217 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN B 99 HIS B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 476 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN F 5 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.244897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.218418 restraints weight = 113811.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.224815 restraints weight = 63422.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.229404 restraints weight = 40341.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.231954 restraints weight = 28034.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.234219 restraints weight = 21369.886| |-----------------------------------------------------------------------------| r_work (final): 0.5135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3841 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 15228 Z= 0.237 Angle : 0.745 27.964 20645 Z= 0.401 Chirality : 0.042 0.169 2265 Planarity : 0.007 0.121 2579 Dihedral : 7.848 85.794 2226 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.36 (0.18), residues: 1775 helix: -0.32 (0.17), residues: 781 sheet: -0.43 (0.39), residues: 179 loop : -1.53 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 38 TYR 0.034 0.002 TYR B 30 PHE 0.029 0.003 PHE A 646 TRP 0.027 0.003 TRP F 96 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (15227) covalent geometry : angle 0.74515 / 0.40 (20643) SS BOND : bond 0.00708 / 0.34 ( 1) SS BOND : angle 0.70901 / 0.41 ( 2) hydrogen bonds : bond 0.05245 / 3.49 ( 727) hydrogen bonds : angle 5.45382 / 3.83 ( 1994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 248 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.743 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: A 182 MET cc_start: -0.3177 (mmp) cc_final: -0.3414 (mmp) REVERT: A 477 MET cc_start: 0.6727 (mpp) cc_final: 0.5990 (mpp) REVERT: A 523 MET cc_start: -0.2066 (mpp) cc_final: -0.2387 (mpp) REVERT: B 141 THR cc_start: 0.5562 (m) cc_final: 0.5263 (m) REVERT: B 260 ARG cc_start: 0.7432 (tmm-80) cc_final: 0.7157 (ttp80) REVERT: B 302 ILE cc_start: 0.5294 (mt) cc_final: 0.5018 (mt) REVERT: B 408 MET cc_start: 0.3834 (tpt) cc_final: 0.3612 (tpt) REVERT: B 560 ARG cc_start: 0.2040 (mpt180) cc_final: 0.1494 (mmt-90) REVERT: C 87 ASP cc_start: 0.4709 (p0) cc_final: 0.4037 (m-30) REVERT: F 36 TRP cc_start: 0.2770 (m100) cc_final: 0.2015 (m100) REVERT: F 64 ARG cc_start: 0.1308 (mmt180) cc_final: 0.0949 (mmt180) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2976 time to fit residues: 103.4487 Evaluate side-chains 223 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 54 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 456 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5307 r_free = 0.5307 target = 0.249386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.224383 restraints weight = 112116.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.230718 restraints weight = 61583.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.235293 restraints weight = 38225.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.238109 restraints weight = 26015.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.239725 restraints weight = 19049.065| |-----------------------------------------------------------------------------| r_work (final): 0.5192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3645 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15228 Z= 0.119 Angle : 0.572 25.684 20645 Z= 0.300 Chirality : 0.038 0.174 2265 Planarity : 0.005 0.087 2579 Dihedral : 7.509 86.371 2226 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.81 (0.19), residues: 1775 helix: 0.32 (0.18), residues: 779 sheet: -0.70 (0.37), residues: 191 loop : -1.31 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 101 TYR 0.023 0.001 TYR B 30 PHE 0.027 0.002 PHE B 9 TRP 0.010 0.001 TRP B 580 HIS 0.005 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15227) covalent geometry : angle 0.57210 / 0.30 (20643) SS BOND : bond 0.00294 / 0.14 ( 1) SS BOND : angle 1.19882 / 0.70 ( 2) hydrogen bonds : bond 0.04117 / 2.74 ( 727) hydrogen bonds : angle 4.95398 / 3.49 ( 1994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 237 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.720 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: A 311 MET cc_start: 0.3317 (tmm) cc_final: 0.3043 (tmm) REVERT: A 477 MET cc_start: 0.6616 (mpp) cc_final: 0.5818 (mpp) REVERT: A 591 GLN cc_start: 0.7311 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 141 THR cc_start: 0.5668 (m) cc_final: 0.5320 (m) REVERT: B 260 ARG cc_start: 0.7213 (tmm-80) cc_final: 0.6819 (ttp80) REVERT: B 302 ILE cc_start: 0.4303 (mt) cc_final: 0.4082 (mt) REVERT: B 372 MET cc_start: 0.3394 (ttm) cc_final: 0.3124 (ttm) REVERT: B 446 ASP cc_start: 0.8377 (m-30) cc_final: 0.8006 (m-30) REVERT: C 50 MET cc_start: 0.7923 (mmt) cc_final: 0.7255 (tpp) REVERT: C 87 ASP cc_start: 0.4598 (p0) cc_final: 0.3970 (m-30) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2857 time to fit residues: 96.5046 Evaluate side-chains 209 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 1 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 455 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.247739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.222091 restraints weight = 113644.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.228616 restraints weight = 63170.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.233275 restraints weight = 39430.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.236101 restraints weight = 26862.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.238101 restraints weight = 19724.741| |-----------------------------------------------------------------------------| r_work (final): 0.5182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3706 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15228 Z= 0.134 Angle : 0.580 27.467 20645 Z= 0.304 Chirality : 0.038 0.172 2265 Planarity : 0.005 0.077 2579 Dihedral : 7.513 88.860 2226 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.73 (0.19), residues: 1775 helix: 0.44 (0.18), residues: 786 sheet: -0.68 (0.37), residues: 191 loop : -1.34 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.016 0.001 TYR B 30 PHE 0.045 0.002 PHE B 9 TRP 0.014 0.001 TRP B 580 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15227) covalent geometry : angle 0.58014 / 0.30 (20643) SS BOND : bond 0.00067 / 0.03 ( 1) SS BOND : angle 0.96224 / 0.57 ( 2) hydrogen bonds : bond 0.04142 / 2.78 ( 727) hydrogen bonds : angle 4.88692 / 3.43 ( 1994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 230 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.586 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 79 ILE cc_start: 0.7677 (mm) cc_final: 0.7437 (mt) REVERT: A 477 MET cc_start: 0.6703 (mpp) cc_final: 0.5910 (mpp) REVERT: A 523 MET cc_start: -0.2380 (mpp) cc_final: -0.2704 (mpp) REVERT: B 141 THR cc_start: 0.5767 (m) cc_final: 0.5439 (m) REVERT: B 302 ILE cc_start: 0.4429 (mt) cc_final: 0.4155 (mt) REVERT: B 372 MET cc_start: 0.3429 (ttm) cc_final: 0.3220 (ttm) REVERT: B 700 PHE cc_start: 0.8191 (m-80) cc_final: 0.7893 (m-80) REVERT: C 50 MET cc_start: 0.7806 (mmt) cc_final: 0.7222 (tpp) REVERT: C 87 ASP cc_start: 0.4644 (p0) cc_final: 0.4007 (m-30) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2834 time to fit residues: 92.7427 Evaluate side-chains 211 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 131 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 chunk 140 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5318 r_free = 0.5318 target = 0.250270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.225254 restraints weight = 119637.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.231666 restraints weight = 67345.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.236064 restraints weight = 42633.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.238864 restraints weight = 29339.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.240830 restraints weight = 21717.564| |-----------------------------------------------------------------------------| r_work (final): 0.5226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3591 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 15228 Z= 0.110 Angle : 0.549 26.759 20645 Z= 0.288 Chirality : 0.038 0.152 2265 Planarity : 0.004 0.074 2579 Dihedral : 7.350 89.882 2226 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.55 (0.19), residues: 1775 helix: 0.64 (0.18), residues: 788 sheet: -0.67 (0.37), residues: 197 loop : -1.28 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.020 0.001 TYR B 497 PHE 0.029 0.002 PHE B 490 TRP 0.009 0.001 TRP B 580 HIS 0.005 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15227) covalent geometry : angle 0.54854 / 0.29 (20643) SS BOND : bond 0.00173 / 0.08 ( 1) SS BOND : angle 0.88512 / 0.52 ( 2) hydrogen bonds : bond 0.03859 / 2.57 ( 727) hydrogen bonds : angle 4.79308 / 3.35 ( 1994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 228 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.670 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: A 79 ILE cc_start: 0.7645 (mm) cc_final: 0.7407 (mt) REVERT: A 477 MET cc_start: 0.6840 (mpp) cc_final: 0.6331 (mpp) REVERT: B 290 MET cc_start: 0.3894 (mmt) cc_final: 0.3608 (mmt) REVERT: B 372 MET cc_start: 0.3438 (ttm) cc_final: 0.3237 (ttm) REVERT: C 50 MET cc_start: 0.7506 (mmt) cc_final: 0.6749 (tpp) REVERT: C 87 ASP cc_start: 0.4171 (p0) cc_final: 0.3736 (m-30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2737 time to fit residues: 89.4776 Evaluate side-chains 209 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 56 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5277 r_free = 0.5277 target = 0.245128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.218799 restraints weight = 120034.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.225030 restraints weight = 69319.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.229363 restraints weight = 44833.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.232209 restraints weight = 31728.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.233999 restraints weight = 23949.843| |-----------------------------------------------------------------------------| r_work (final): 0.5130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3876 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15228 Z= 0.177 Angle : 0.632 26.817 20645 Z= 0.336 Chirality : 0.039 0.169 2265 Planarity : 0.005 0.091 2579 Dihedral : 7.624 92.983 2226 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.86 (0.19), residues: 1775 helix: 0.26 (0.18), residues: 792 sheet: -0.77 (0.37), residues: 191 loop : -1.33 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 151 TYR 0.023 0.002 TYR B 30 PHE 0.034 0.003 PHE B 9 TRP 0.025 0.002 TRP F 96 HIS 0.005 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (15227) covalent geometry : angle 0.63217 / 0.34 (20643) SS BOND : bond 0.00444 / 0.21 ( 1) SS BOND : angle 0.77125 / 0.45 ( 2) hydrogen bonds : bond 0.04510 / 3.02 ( 727) hydrogen bonds : angle 5.09308 / 3.55 ( 1994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 225 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.703 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: A 79 ILE cc_start: 0.7801 (mm) cc_final: 0.7554 (mt) REVERT: A 182 MET cc_start: -0.3561 (mmp) cc_final: -0.3776 (mmp) REVERT: A 477 MET cc_start: 0.6773 (mpp) cc_final: 0.5942 (mpp) REVERT: A 523 MET cc_start: -0.2576 (mpp) cc_final: -0.2816 (mpp) REVERT: B 69 ILE cc_start: 0.7980 (mm) cc_final: 0.7773 (mm) REVERT: B 227 MET cc_start: 0.3779 (pmm) cc_final: 0.3489 (pmm) REVERT: B 484 ILE cc_start: 0.3870 (tt) cc_final: 0.3625 (tt) REVERT: B 700 PHE cc_start: 0.8552 (m-10) cc_final: 0.8334 (m-10) REVERT: C 50 MET cc_start: 0.7932 (mmt) cc_final: 0.7614 (mmt) REVERT: C 53 MET cc_start: 0.4174 (mmt) cc_final: 0.3958 (mmt) REVERT: C 87 ASP cc_start: 0.4754 (p0) cc_final: 0.4195 (m-30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2761 time to fit residues: 88.4101 Evaluate side-chains 207 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 172 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 442 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.5233 r_free = 0.5233 target = 0.239985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.214413 restraints weight = 110585.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.220602 restraints weight = 61913.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.224965 restraints weight = 39358.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.227726 restraints weight = 27320.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.229389 restraints weight = 20524.778| |-----------------------------------------------------------------------------| r_work (final): 0.5105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4042 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 15228 Z= 0.219 Angle : 0.713 26.753 20645 Z= 0.384 Chirality : 0.042 0.198 2265 Planarity : 0.006 0.086 2579 Dihedral : 8.174 97.155 2226 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.33 (0.19), residues: 1775 helix: -0.24 (0.18), residues: 785 sheet: -0.56 (0.40), residues: 171 loop : -1.56 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 151 TYR 0.046 0.002 TYR B 30 PHE 0.040 0.003 PHE B 9 TRP 0.027 0.003 TRP B 438 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (15227) covalent geometry : angle 0.71323 / 0.38 (20643) SS BOND : bond 0.00279 / 0.13 ( 1) SS BOND : angle 1.00285 / 0.59 ( 2) hydrogen bonds : bond 0.05122 / 3.45 ( 727) hydrogen bonds : angle 5.50642 / 3.85 ( 1994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.65 seconds wall clock time: 89 minutes 3.21 seconds (5343.21 seconds total)