Starting phenix.real_space_refine on Fri Mar 6 06:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nk1_12428/03_2026/7nk1_12428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk1_12428/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nk1_12428/03_2026/7nk1_12428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk1_12428/03_2026/7nk1_12428.map" model { file = "/net/cci-nas-00/data/ceres_data/7nk1_12428/03_2026/7nk1_12428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk1_12428/03_2026/7nk1_12428.cif" } 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-5986/lib/python3.9/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: 4.79, per 1000 atoms: 0.17 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: 2.24 Conformation dependent library (CDL) restraints added in 893.8 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: 5.04 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: 7.00 Time building geometry restraints manager: 2.90 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: 12542 17.94 - 35.88: 861 35.88 - 53.81: 253 53.81 - 71.75: 89 71.75 - 89.69: 16 Dihedral angle restraints: 13761 sinusoidal: 7724 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 13758 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: 1.080 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.780 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2043 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 : 14.324 89.689 5954 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 covalent geometry : bond 0.00402 (15227) covalent geometry : angle 0.68913 (20643) SS BOND : bond 0.02507 ( 1) SS BOND : angle 5.06722 ( 2) hydrogen bonds : bond 0.15070 ( 727) hydrogen bonds : angle 5.96927 ( 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 : 0.573 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: 0.3222 time to fit residues: 149.1019 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 : 0.711 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 703 ASN B 134 ASN B 312 ASN B 425 ASN B 456 HIS B 676 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5414 r_free = 0.5414 target = 0.265175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.244555 restraints weight = 108122.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.250812 restraints weight = 56758.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.254756 restraints weight = 32829.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.257382 restraints weight = 21115.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.259106 restraints weight = 14645.671| |-----------------------------------------------------------------------------| r_work (final): 0.5337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3034 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15228 Z= 0.179 Angle : 0.646 27.418 20645 Z= 0.341 Chirality : 0.039 0.169 2265 Planarity : 0.005 0.071 2579 Dihedral : 10.176 73.215 2304 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 0.35 (0.19), residues: 778 sheet: -0.61 (0.39), residues: 186 loop : -1.13 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 706 TYR 0.023 0.002 TYR C 111 PHE 0.023 0.002 PHE B 696 TRP 0.016 0.002 TRP F 96 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00364 (15227) covalent geometry : angle 0.64559 (20643) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.25654 ( 2) hydrogen bonds : bond 0.04707 ( 727) hydrogen bonds : angle 5.12039 ( 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 248 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.516 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: 0.6378 (mpp) cc_final: 0.6173 (mpp) REVERT: A 523 MET cc_start: -0.2103 (mpp) cc_final: -0.2441 (mpp) REVERT: B 141 THR cc_start: 0.6007 (m) cc_final: 0.5745 (m) REVERT: B 290 MET cc_start: 0.5146 (tpt) cc_final: 0.4694 (tpt) REVERT: B 372 MET cc_start: 0.2462 (ttm) cc_final: 0.2233 (ttm) REVERT: B 408 MET cc_start: 0.2623 (tpt) cc_final: 0.2141 (tpt) REVERT: B 507 MET cc_start: 0.6361 (mmp) cc_final: 0.6098 (mmp) REVERT: C 87 ASP cc_start: 0.3843 (p0) cc_final: 0.2866 (m-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3231 time to fit residues: 111.3114 Evaluate side-chains 204 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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: 6.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN B 335 ASN B 425 ASN B 756 GLN F 39 GLN ** 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 = 0.5413 r_free = 0.5413 target = 0.263352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.241867 restraints weight = 118343.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.248158 restraints weight = 63498.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.252290 restraints weight = 37869.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.254914 restraints weight = 25019.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.256760 restraints weight = 17628.399| |-----------------------------------------------------------------------------| r_work (final): 0.5355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3050 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15228 Z= 0.123 Angle : 0.560 26.299 20645 Z= 0.292 Chirality : 0.037 0.151 2265 Planarity : 0.004 0.079 2579 Dihedral : 10.013 73.218 2304 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1775 helix: 0.40 (0.18), residues: 797 sheet: -0.54 (0.37), residues: 201 loop : -1.17 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.016 0.001 TYR B 620 PHE 0.017 0.001 PHE C 119 TRP 0.012 0.001 TRP F 96 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00274 (15227) covalent geometry : angle 0.55967 (20643) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.65234 ( 2) hydrogen bonds : bond 0.04346 ( 727) hydrogen bonds : angle 4.89298 ( 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 234 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.734 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 477 MET cc_start: 0.6267 (mpp) cc_final: 0.5935 (mpp) REVERT: B 141 THR cc_start: 0.5892 (m) cc_final: 0.5665 (m) REVERT: B 290 MET cc_start: 0.4885 (tpt) cc_final: 0.4569 (tpp) REVERT: B 372 MET cc_start: 0.2651 (ttm) cc_final: 0.2420 (ttm) REVERT: B 408 MET cc_start: 0.3122 (tpt) cc_final: 0.2570 (tpt) REVERT: C 53 MET cc_start: 0.3317 (mmt) cc_final: 0.3061 (mmt) REVERT: C 87 ASP cc_start: 0.3222 (p0) cc_final: 0.2433 (m-30) REVERT: F 64 ARG cc_start: 0.2265 (mmt180) cc_final: 0.1938 (mmt180) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.3327 time to fit residues: 109.0631 Evaluate side-chains 205 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 169 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 73 GLN ** C 242 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.253094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.229744 restraints weight = 108126.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.236118 restraints weight = 58518.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.240635 restraints weight = 35682.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.243518 restraints weight = 23771.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.5249 r_free = 0.5249 target = 0.245520 restraints weight = 16987.453| |-----------------------------------------------------------------------------| r_work (final): 0.5238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3562 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15228 Z= 0.212 Angle : 0.689 27.921 20645 Z= 0.367 Chirality : 0.040 0.165 2265 Planarity : 0.006 0.094 2579 Dihedral : 10.369 74.175 2304 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.13 % Allowed : 2.15 % 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: -1.03 (0.19), residues: 1775 helix: -0.08 (0.18), residues: 802 sheet: -0.50 (0.38), residues: 195 loop : -1.31 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 312 TYR 0.026 0.002 TYR B 559 PHE 0.025 0.002 PHE B 496 TRP 0.021 0.002 TRP B 580 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00463 (15227) covalent geometry : angle 0.68898 (20643) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.18359 ( 2) hydrogen bonds : bond 0.04959 ( 727) hydrogen bonds : angle 5.17835 ( 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 251 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.726 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: A 79 ILE cc_start: 0.7981 (mm) cc_final: 0.7375 (mt) REVERT: A 182 MET cc_start: -0.3424 (mmp) cc_final: -0.3645 (mmp) REVERT: A 523 MET cc_start: -0.2104 (mpp) cc_final: -0.2487 (mpp) REVERT: B 141 THR cc_start: 0.5882 (m) cc_final: 0.5227 (m) REVERT: B 372 MET cc_start: 0.3060 (ttm) cc_final: 0.2800 (ttm) REVERT: B 407 MET cc_start: 0.2942 (ttp) cc_final: 0.2722 (ttm) REVERT: B 408 MET cc_start: 0.3218 (tpt) cc_final: 0.2471 (tpt) REVERT: B 645 MET cc_start: 0.3263 (mmm) cc_final: 0.2906 (mmp) REVERT: C 87 ASP cc_start: 0.4291 (p0) cc_final: 0.3538 (m-30) REVERT: C 202 MET cc_start: 0.6902 (mmm) cc_final: 0.6573 (mmm) REVERT: C 218 LEU cc_start: 0.7997 (mm) cc_final: 0.7780 (mm) REVERT: F 64 ARG cc_start: 0.1528 (mmt180) cc_final: 0.1084 (mmt180) outliers start: 2 outliers final: 1 residues processed: 251 average time/residue: 0.3332 time to fit residues: 116.8632 Evaluate side-chains 222 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 8.9990 chunk 57 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.255665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.232499 restraints weight = 118734.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.238863 restraints weight = 65575.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.243219 restraints weight = 40360.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.246113 restraints weight = 27085.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.247895 restraints weight = 19344.443| |-----------------------------------------------------------------------------| r_work (final): 0.5247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3466 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15228 Z= 0.120 Angle : 0.563 26.815 20645 Z= 0.296 Chirality : 0.038 0.160 2265 Planarity : 0.005 0.095 2579 Dihedral : 10.228 75.773 2304 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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: -0.63 (0.19), residues: 1775 helix: 0.33 (0.18), residues: 792 sheet: -0.51 (0.37), residues: 197 loop : -1.11 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 124 TYR 0.024 0.001 TYR B 30 PHE 0.018 0.002 PHE C 217 TRP 0.012 0.001 TRP B 580 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00267 (15227) covalent geometry : angle 0.56302 (20643) SS BOND : bond 0.00139 ( 1) SS BOND : angle 1.13303 ( 2) hydrogen bonds : bond 0.04137 ( 727) hydrogen bonds : angle 4.87693 ( 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 237 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: -0.3440 (mmp) cc_final: -0.3645 (mmp) REVERT: A 477 MET cc_start: 0.6487 (mpp) cc_final: 0.6166 (mpp) REVERT: B 69 ILE cc_start: 0.7799 (mm) cc_final: 0.7588 (mm) REVERT: B 356 MET cc_start: 0.4445 (tpp) cc_final: 0.4110 (tpp) REVERT: B 372 MET cc_start: 0.3038 (ttm) cc_final: 0.2769 (ttm) REVERT: B 408 MET cc_start: 0.3225 (tpt) cc_final: 0.2454 (tpt) REVERT: B 645 MET cc_start: 0.3146 (mmm) cc_final: 0.2462 (mmm) REVERT: C 87 ASP cc_start: 0.4488 (p0) cc_final: 0.3817 (m-30) REVERT: F 64 ARG cc_start: 0.1127 (mmt180) cc_final: 0.0712 (mmt180) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3247 time to fit residues: 106.4123 Evaluate side-chains 221 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 73 GLN F 5 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.247688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.221780 restraints weight = 112581.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.228310 restraints weight = 62990.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.232962 restraints weight = 39594.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.235547 restraints weight = 26980.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.237778 restraints weight = 20263.129| |-----------------------------------------------------------------------------| r_work (final): 0.5172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3821 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15228 Z= 0.201 Angle : 0.679 25.990 20645 Z= 0.364 Chirality : 0.040 0.173 2265 Planarity : 0.006 0.079 2579 Dihedral : 10.561 82.059 2304 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -1.06 (0.19), residues: 1775 helix: -0.04 (0.18), residues: 782 sheet: -0.56 (0.37), residues: 196 loop : -1.36 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 116 TYR 0.029 0.002 TYR B 30 PHE 0.030 0.003 PHE B 466 TRP 0.024 0.002 TRP B 580 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00444 (15227) covalent geometry : angle 0.67937 (20643) SS BOND : bond 0.00426 ( 1) SS BOND : angle 0.70087 ( 2) hydrogen bonds : bond 0.04823 ( 727) hydrogen bonds : angle 5.18369 ( 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 249 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.761 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 86 MET cc_start: 0.4263 (mmm) cc_final: 0.3939 (tpt) REVERT: A 182 MET cc_start: -0.3249 (mmp) cc_final: -0.3488 (mmp) REVERT: A 360 MET cc_start: 0.1940 (ttt) cc_final: 0.1298 (ttt) REVERT: A 477 MET cc_start: 0.6736 (mpp) cc_final: 0.5935 (mpp) REVERT: B 141 THR cc_start: 0.5496 (m) cc_final: 0.5229 (m) REVERT: B 372 MET cc_start: 0.3301 (ttm) cc_final: 0.3085 (ttm) REVERT: B 408 MET cc_start: 0.3549 (tpt) cc_final: 0.2699 (tpt) REVERT: B 679 GLN cc_start: 0.6148 (mm-40) cc_final: 0.5929 (mp10) REVERT: C 87 ASP cc_start: 0.4647 (p0) cc_final: 0.3975 (m-30) REVERT: F 34 MET cc_start: 0.6517 (tpt) cc_final: 0.6275 (tpp) REVERT: F 64 ARG cc_start: 0.1056 (mmt180) cc_final: 0.0666 (mmt180) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3536 time to fit residues: 121.5129 Evaluate side-chains 224 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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: 6.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.245058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.219109 restraints weight = 119318.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.225398 restraints weight = 67385.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.229915 restraints weight = 43308.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 76)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.232720 restraints weight = 30119.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.234721 restraints weight = 22577.092| |-----------------------------------------------------------------------------| r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3933 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 15228 Z= 0.205 Angle : 0.695 28.178 20645 Z= 0.368 Chirality : 0.041 0.220 2265 Planarity : 0.006 0.090 2579 Dihedral : 10.693 86.109 2304 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1775 helix: -0.12 (0.18), residues: 775 sheet: -0.53 (0.39), residues: 173 loop : -1.40 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 623 TYR 0.027 0.002 TYR B 30 PHE 0.062 0.003 PHE A 503 TRP 0.019 0.002 TRP B 580 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00459 (15227) covalent geometry : angle 0.69508 (20643) SS BOND : bond 0.00359 ( 1) SS BOND : angle 0.85640 ( 2) hydrogen bonds : bond 0.04890 ( 727) hydrogen bonds : angle 5.31606 ( 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 242 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.729 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: B 141 THR cc_start: 0.5825 (m) cc_final: 0.5485 (m) REVERT: B 302 ILE cc_start: 0.4907 (mt) cc_final: 0.4643 (mt) REVERT: B 356 MET cc_start: 0.5221 (tpp) cc_final: 0.4996 (tpp) REVERT: B 408 MET cc_start: 0.4138 (tpt) cc_final: 0.3392 (tpt) REVERT: B 446 ASP cc_start: 0.8319 (m-30) cc_final: 0.7936 (m-30) REVERT: C 87 ASP cc_start: 0.4539 (p0) cc_final: 0.3994 (m-30) REVERT: F 64 ARG cc_start: 0.0875 (mmt180) cc_final: 0.0630 (mmt180) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3307 time to fit residues: 110.7334 Evaluate side-chains 222 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 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: 0.9980 chunk 164 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN 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 582 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 = 0.5289 r_free = 0.5289 target = 0.246716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.222261 restraints weight = 110934.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.228750 restraints weight = 60406.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.233295 restraints weight = 37362.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.236114 restraints weight = 25174.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.237766 restraints weight = 18333.266| |-----------------------------------------------------------------------------| r_work (final): 0.5178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3814 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15228 Z= 0.134 Angle : 0.602 26.741 20645 Z= 0.312 Chirality : 0.038 0.171 2265 Planarity : 0.005 0.092 2579 Dihedral : 10.569 87.243 2304 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.90 (0.19), residues: 1775 helix: 0.25 (0.18), residues: 786 sheet: -0.85 (0.37), residues: 188 loop : -1.34 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.027 0.001 TYR B 30 PHE 0.021 0.002 PHE A 503 TRP 0.011 0.001 TRP B 438 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00306 (15227) covalent geometry : angle 0.60231 (20643) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.88866 ( 2) hydrogen bonds : bond 0.04230 ( 727) hydrogen bonds : angle 4.99983 ( 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 237 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.7676 (mm) cc_final: 0.7434 (mt) REVERT: A 311 MET cc_start: 0.3548 (tmm) cc_final: 0.3242 (tmm) REVERT: A 360 MET cc_start: 0.2454 (ttt) cc_final: 0.1933 (ttt) REVERT: B 69 ILE cc_start: 0.7855 (mm) cc_final: 0.7653 (mm) REVERT: B 141 THR cc_start: 0.5703 (m) cc_final: 0.5361 (m) REVERT: B 302 ILE cc_start: 0.4643 (mt) cc_final: 0.4434 (mt) REVERT: B 372 MET cc_start: 0.3566 (ttm) cc_final: 0.3339 (ttm) REVERT: B 408 MET cc_start: 0.3879 (tpt) cc_final: 0.3160 (tpt) REVERT: B 446 ASP cc_start: 0.8304 (m-30) cc_final: 0.7923 (m-30) REVERT: C 50 MET cc_start: 0.7885 (mmt) cc_final: 0.7212 (tpp) REVERT: C 87 ASP cc_start: 0.4586 (p0) cc_final: 0.3963 (m-30) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3535 time to fit residues: 115.9555 Evaluate side-chains 217 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 582 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.240240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.214562 restraints weight = 110193.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.220712 restraints weight = 61832.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.225064 restraints weight = 39513.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.227643 restraints weight = 27714.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.229883 restraints weight = 21135.237| |-----------------------------------------------------------------------------| r_work (final): 0.5107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4112 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 15228 Z= 0.234 Angle : 0.733 27.112 20645 Z= 0.394 Chirality : 0.042 0.227 2265 Planarity : 0.006 0.094 2579 Dihedral : 10.901 91.981 2304 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % 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: -1.45 (0.19), residues: 1775 helix: -0.28 (0.17), residues: 792 sheet: -0.62 (0.40), residues: 167 loop : -1.68 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 233 TYR 0.026 0.002 TYR B 30 PHE 0.032 0.003 PHE B 496 TRP 0.032 0.003 TRP F 108 HIS 0.007 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00517 (15227) covalent geometry : angle 0.73290 (20643) SS BOND : bond 0.00560 ( 1) SS BOND : angle 0.71597 ( 2) hydrogen bonds : bond 0.05283 ( 727) hydrogen bonds : angle 5.51660 ( 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 238 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.773 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: B 302 ILE cc_start: 0.5161 (mt) cc_final: 0.4876 (mt) REVERT: B 372 MET cc_start: 0.3935 (ttm) cc_final: 0.3642 (ttm) REVERT: B 446 ASP cc_start: 0.8086 (m-30) cc_final: 0.7700 (m-30) REVERT: B 623 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6528 (mtt90) REVERT: C 87 ASP cc_start: 0.4364 (p0) cc_final: 0.3880 (m-30) REVERT: F 36 TRP cc_start: 0.2871 (m100) cc_final: 0.2585 (m100) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3526 time to fit residues: 115.2261 Evaluate side-chains 217 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 4.9990 chunk 148 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 29 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 233 HIS ** 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 = 0.5266 r_free = 0.5266 target = 0.244136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.219216 restraints weight = 110966.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.225486 restraints weight = 62327.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.229896 restraints weight = 39754.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.232701 restraints weight = 27469.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.234644 restraints weight = 20443.525| |-----------------------------------------------------------------------------| r_work (final): 0.5161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3965 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15228 Z= 0.142 Angle : 0.620 26.806 20645 Z= 0.326 Chirality : 0.039 0.192 2265 Planarity : 0.005 0.090 2579 Dihedral : 10.765 91.964 2304 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1775 helix: 0.08 (0.18), residues: 792 sheet: -0.79 (0.38), residues: 173 loop : -1.59 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 260 TYR 0.028 0.002 TYR B 30 PHE 0.036 0.002 PHE B 490 TRP 0.016 0.002 TRP B 438 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00322 (15227) covalent geometry : angle 0.62042 (20643) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.13750 ( 2) hydrogen bonds : bond 0.04400 ( 727) hydrogen bonds : angle 5.15542 ( 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 234 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.147 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: A 523 MET cc_start: -0.2911 (mpp) cc_final: -0.3570 (pmm) REVERT: B 133 LEU cc_start: 0.8127 (mm) cc_final: 0.7924 (tp) REVERT: B 302 ILE cc_start: 0.4851 (mt) cc_final: 0.4626 (mt) REVERT: B 372 MET cc_start: 0.3996 (ttm) cc_final: 0.3694 (ttm) REVERT: B 623 ARG cc_start: 0.7344 (mtt180) cc_final: 0.7008 (mtt180) REVERT: C 50 MET cc_start: 0.7899 (mmt) cc_final: 0.7490 (mmt) REVERT: C 87 ASP cc_start: 0.4122 (p0) cc_final: 0.3860 (m-30) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3538 time to fit residues: 113.5494 Evaluate side-chains 210 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 8.9990 chunk 159 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** 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 = 0.5220 r_free = 0.5220 target = 0.238333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.211991 restraints weight = 114015.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.218165 restraints weight = 65002.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.222536 restraints weight = 42035.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.225051 restraints weight = 29773.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.227251 restraints weight = 22949.459| |-----------------------------------------------------------------------------| r_work (final): 0.5088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4219 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15228 Z= 0.235 Angle : 0.737 26.729 20645 Z= 0.396 Chirality : 0.042 0.225 2265 Planarity : 0.006 0.092 2579 Dihedral : 11.124 95.063 2304 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.65 (0.19), residues: 1775 helix: -0.43 (0.17), residues: 792 sheet: -0.90 (0.40), residues: 169 loop : -1.77 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 38 TYR 0.044 0.002 TYR B 30 PHE 0.040 0.003 PHE B 496 TRP 0.033 0.003 TRP F 108 HIS 0.010 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00520 (15227) covalent geometry : angle 0.73694 (20643) SS BOND : bond 0.00604 ( 1) SS BOND : angle 0.88252 ( 2) hydrogen bonds : bond 0.05322 ( 727) hydrogen bonds : angle 5.63535 ( 1994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5726.33 seconds wall clock time: 98 minutes 19.04 seconds (5899.04 seconds total)