Starting phenix.real_space_refine on Sun Jul 5 15:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj5_12373/07_2026/7nj5_12373.map" } resolution = 4.63 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= 0.032 sd= 0.275 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 9327 2.51 5 N 2602 2.21 5 O 2880 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28806 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: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 96} Chain breaks: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.16 Number of scatterers: 28806 At special positions: 0 Unit cell: (102, 110, 162, 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 2880 8.00 N 2602 7.00 C 9327 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 674.9 milliseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.4% alpha, 15.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.141A 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: 5.020A 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: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A 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: 3.733A 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: 3.530A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A 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: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A 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: 4.330A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A 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: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.658A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A 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: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A 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: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A 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: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A 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: 3.516A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.635A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.974A 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: 3.881A 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 4 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 33 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 646 1.23 - 1.43: 5875 1.43 - 1.63: 8610 1.63 - 1.83: 183 Bond restraints: 29155 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.522 -0.064 1.40e-02 5.10e+03 2.12e+01 bond pdb=" CE1 HIS F 59 " pdb=" NE2 HIS F 59 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.21e+01 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.40e-02 5.10e+03 1.07e+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 9.96e+00 bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.44e+00 ... (remaining 29150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52287 5.65 - 11.30: 19 11.30 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.24: 5 Bond angle restraints: 52312 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 79.76 28.24 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 80.35 27.65 3.00e+00 1.11e-01 8.50e+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 81.83 27.17 3.00e+00 1.11e-01 8.20e+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 82.45 26.55 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 111.90 138.76 -26.86 3.20e+00 9.77e-02 7.05e+01 ... (remaining 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12538 17.93 - 35.85: 849 35.85 - 53.78: 237 53.78 - 71.71: 69 71.71 - 89.63: 11 Dihedral angle restraints: 13704 sinusoidal: 7642 harmonic: 6062 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 137.99 -15.19 0 2.50e+00 1.60e-01 3.69e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 13701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2205 0.112 - 0.225: 58 0.225 - 0.337: 4 0.337 - 0.450: 2 0.450 - 0.562: 1 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 2267 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 94 " -0.017 2.00e-02 2.50e+03 4.95e-02 4.90e+01 pdb=" CG TYR F 94 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 94 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 94 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR F 94 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR F 94 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR F 94 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " 0.017 2.00e-02 2.50e+03 4.83e-02 4.67e+01 pdb=" CG TYR F 32 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 115 " 0.070 2.00e-02 2.50e+03 3.40e-02 2.89e+01 pdb=" CG TRP F 115 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP F 115 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP F 115 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 115 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP F 115 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 115 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 115 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 115 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP F 115 " 0.031 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56261 2.78 - 3.39: 80851 3.39 - 3.99: 105858 3.99 - 4.60: 165202 Nonbonded interactions: 409434 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 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 0.064 15287 Z= 0.245 Angle : 0.731 26.860 20719 Z= 0.431 Chirality : 0.046 0.562 2270 Planarity : 0.005 0.090 2589 Dihedral : 13.590 89.632 5895 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.32 % Allowed : 0.25 % Favored : 99.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.45 (0.19), residues: 786 sheet: -0.71 (0.36), residues: 183 loop : -1.31 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG F 72 TYR 0.094 0.003 TYR F 94 PHE 0.048 0.002 PHE A 446 TRP 0.070 0.002 TRP F 115 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.25 (15287) covalent geometry : angle 0.73068 / 0.43 (20719) hydrogen bonds : bond 0.15249 / 9.93 ( 732) hydrogen bonds : angle 6.05058 / 4.34 ( 2015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 407 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 402 time to evaluate : 0.787 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 483 ILE cc_start: 0.8127 (mt) cc_final: 0.7822 (tp) REVERT: A 522 SER cc_start: 0.8326 (m) cc_final: 0.8107 (t) REVERT: A 528 THR cc_start: 0.7468 (m) cc_final: 0.7147 (p) REVERT: A 540 TYR cc_start: 0.7099 (m-80) cc_final: 0.6881 (m-80) REVERT: A 633 ILE cc_start: 0.6113 (tt) cc_final: 0.5735 (tp) REVERT: A 648 SER cc_start: 0.9094 (t) cc_final: 0.8487 (m) REVERT: B 40 MET cc_start: 0.8049 (mtm) cc_final: 0.7275 (ttm) REVERT: B 229 LYS cc_start: 0.8336 (tttp) cc_final: 0.8134 (ttmm) REVERT: B 407 MET cc_start: 0.6422 (mmm) cc_final: 0.5916 (tpp) REVERT: B 446 ASP cc_start: 0.9092 (m-30) cc_final: 0.8690 (m-30) REVERT: B 509 LEU cc_start: 0.9586 (tp) cc_final: 0.9382 (tp) REVERT: B 561 CYS cc_start: 0.5949 (p) cc_final: 0.5123 (p) REVERT: B 568 ILE cc_start: 0.8315 (mt) cc_final: 0.7776 (tt) REVERT: B 612 LYS cc_start: 0.7594 (mttt) cc_final: 0.6572 (mttt) REVERT: C 42 ASN cc_start: 0.8592 (t0) cc_final: 0.7403 (p0) REVERT: F 12 VAL cc_start: -0.2206 (OUTLIER) cc_final: -0.2686 (m) outliers start: 5 outliers final: 1 residues processed: 406 average time/residue: 0.2682 time to fit residues: 158.0828 Evaluate side-chains 261 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 HIS ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** F 120 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 = 0.4447 r_free = 0.4447 target = 0.135079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.113362 restraints weight = 165863.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.118990 restraints weight = 83830.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.122860 restraints weight = 48990.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.125369 restraints weight = 31602.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.126891 restraints weight = 22128.719| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15287 Z= 0.160 Angle : 0.608 27.500 20719 Z= 0.323 Chirality : 0.039 0.163 2270 Planarity : 0.005 0.057 2589 Dihedral : 6.754 61.632 2236 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.35 (0.18), residues: 787 sheet: -0.51 (0.37), residues: 191 loop : -1.23 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 72 TYR 0.032 0.002 TYR B 217 PHE 0.027 0.002 PHE A 446 TRP 0.010 0.001 TRP A 422 HIS 0.012 0.002 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (15287) covalent geometry : angle 0.60846 / 0.32 (20719) hydrogen bonds : bond 0.04643 / 3.05 ( 732) hydrogen bonds : angle 5.06074 / 3.60 ( 2015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.478 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.7919 (m-80) cc_final: 0.6970 (m-80) REVERT: A 477 MET cc_start: 0.8846 (pmm) cc_final: 0.8455 (mtt) REVERT: A 483 ILE cc_start: 0.8978 (mt) cc_final: 0.8597 (tp) REVERT: A 528 THR cc_start: 0.7916 (m) cc_final: 0.7497 (p) REVERT: A 579 MET cc_start: 0.7788 (tmm) cc_final: 0.7312 (tmm) REVERT: A 633 ILE cc_start: 0.6073 (tt) cc_final: 0.5638 (tp) REVERT: A 648 SER cc_start: 0.9059 (t) cc_final: 0.8310 (m) REVERT: B 3 VAL cc_start: 0.6829 (t) cc_final: 0.6267 (t) REVERT: B 229 LYS cc_start: 0.8648 (tttp) cc_final: 0.8447 (ttmm) REVERT: B 407 MET cc_start: 0.6685 (mmm) cc_final: 0.5982 (tpp) REVERT: B 493 THR cc_start: 0.7814 (m) cc_final: 0.7558 (m) REVERT: B 494 SER cc_start: 0.8107 (p) cc_final: 0.7380 (p) REVERT: B 509 LEU cc_start: 0.9491 (tp) cc_final: 0.9203 (mt) REVERT: B 523 MET cc_start: 0.6269 (tpp) cc_final: 0.5926 (mmm) REVERT: B 561 CYS cc_start: 0.5537 (p) cc_final: 0.4857 (p) REVERT: B 568 ILE cc_start: 0.8660 (mt) cc_final: 0.8102 (tt) REVERT: B 656 GLU cc_start: 0.8815 (tt0) cc_final: 0.8523 (tt0) REVERT: B 685 ASP cc_start: 0.7793 (t0) cc_final: 0.7592 (t70) REVERT: B 718 MET cc_start: 0.8509 (mtm) cc_final: 0.7311 (mmm) REVERT: C 23 THR cc_start: 0.8822 (m) cc_final: 0.8465 (p) REVERT: C 42 ASN cc_start: 0.8583 (t0) cc_final: 0.7353 (p0) REVERT: C 66 MET cc_start: 0.6404 (mmp) cc_final: 0.6175 (mmm) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2485 time to fit residues: 108.1473 Evaluate side-chains 239 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 19 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 GLN B 292 ASN B 313 GLN B 582 GLN B 605 HIS ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 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 = 0.4242 r_free = 0.4242 target = 0.120793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099449 restraints weight = 171545.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.104244 restraints weight = 88304.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.107480 restraints weight = 53140.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.109599 restraints weight = 35778.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.111065 restraints weight = 26532.990| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 15287 Z= 0.272 Angle : 0.741 25.479 20719 Z= 0.403 Chirality : 0.041 0.312 2270 Planarity : 0.008 0.216 2589 Dihedral : 7.353 68.507 2236 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.40 (0.18), residues: 1784 helix: -0.37 (0.17), residues: 797 sheet: -0.77 (0.34), residues: 210 loop : -1.48 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 142 TYR 0.023 0.002 TYR A 130 PHE 0.053 0.003 PHE B 412 TRP 0.032 0.003 TRP C 99 HIS 0.017 0.002 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.27 (15287) covalent geometry : angle 0.74146 / 0.40 (20719) hydrogen bonds : bond 0.04975 / 3.29 ( 732) hydrogen bonds : angle 5.42411 / 3.87 ( 2015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 262 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.8322 (mtm) cc_final: 0.7903 (mtm) REVERT: A 477 MET cc_start: 0.8836 (pmm) cc_final: 0.8573 (mpp) REVERT: A 579 MET cc_start: 0.8335 (tmm) cc_final: 0.7238 (tmm) REVERT: B 229 LYS cc_start: 0.8758 (tttp) cc_final: 0.8311 (ttpt) REVERT: B 407 MET cc_start: 0.8463 (mmm) cc_final: 0.7393 (mmm) REVERT: B 507 MET cc_start: 0.7954 (mmm) cc_final: 0.7550 (mmm) REVERT: B 546 MET cc_start: 0.8858 (mmm) cc_final: 0.8526 (mmt) REVERT: B 559 TYR cc_start: 0.7542 (m-80) cc_final: 0.7041 (m-10) REVERT: B 568 ILE cc_start: 0.8994 (mt) cc_final: 0.8098 (tp) REVERT: B 620 TYR cc_start: 0.6174 (t80) cc_final: 0.5722 (t80) REVERT: B 690 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7983 (tm-30) REVERT: B 724 ILE cc_start: 0.9006 (mm) cc_final: 0.8769 (tp) REVERT: C 7 LEU cc_start: 0.8266 (tt) cc_final: 0.7977 (tt) REVERT: C 23 THR cc_start: 0.8988 (m) cc_final: 0.8712 (p) REVERT: F 34 MET cc_start: -0.0456 (mpp) cc_final: -0.0720 (mmt) REVERT: F 83 MET cc_start: 0.8061 (mpp) cc_final: 0.7614 (mpp) outliers start: 2 outliers final: 0 residues processed: 262 average time/residue: 0.2439 time to fit residues: 97.4048 Evaluate side-chains 208 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 713 HIS ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.123078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.100932 restraints weight = 167114.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105990 restraints weight = 83443.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.109412 restraints weight = 49522.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.111717 restraints weight = 33055.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.113291 restraints weight = 24123.930| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15287 Z= 0.119 Angle : 0.564 27.678 20719 Z= 0.295 Chirality : 0.038 0.157 2270 Planarity : 0.005 0.110 2589 Dihedral : 7.003 71.409 2236 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1784 helix: 0.35 (0.18), residues: 788 sheet: -0.34 (0.38), residues: 184 loop : -1.35 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 124 TYR 0.011 0.001 TYR A 130 PHE 0.020 0.001 PHE B 730 TRP 0.010 0.001 TRP B 666 HIS 0.008 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15287) covalent geometry : angle 0.56423 / 0.29 (20719) hydrogen bonds : bond 0.03995 / 2.63 ( 732) hydrogen bonds : angle 4.85259 / 3.46 ( 2015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 259 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.706 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 97 THR cc_start: 0.8098 (p) cc_final: 0.7871 (p) REVERT: A 334 TYR cc_start: 0.8554 (m-80) cc_final: 0.7772 (m-80) REVERT: A 360 MET cc_start: 0.8118 (mtm) cc_final: 0.7633 (mpp) REVERT: A 459 ILE cc_start: 0.7673 (mt) cc_final: 0.7428 (mt) REVERT: A 477 MET cc_start: 0.8792 (pmm) cc_final: 0.8542 (mtp) REVERT: B 174 MET cc_start: 0.5674 (ttp) cc_final: 0.5348 (ttm) REVERT: B 229 LYS cc_start: 0.8679 (tttp) cc_final: 0.8276 (ttpt) REVERT: B 507 MET cc_start: 0.7642 (mmm) cc_final: 0.7412 (mmm) REVERT: B 559 TYR cc_start: 0.7131 (m-80) cc_final: 0.6830 (m-10) REVERT: B 690 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7986 (tm-30) REVERT: C 23 THR cc_start: 0.9028 (m) cc_final: 0.8754 (p) REVERT: C 161 ASP cc_start: 0.8706 (m-30) cc_final: 0.8498 (m-30) REVERT: F 94 TYR cc_start: 0.8429 (m-80) cc_final: 0.8183 (m-80) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2369 time to fit residues: 95.0802 Evaluate side-chains 216 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 101 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 670 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.112250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091062 restraints weight = 182460.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.095330 restraints weight = 94391.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.098196 restraints weight = 57981.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.100171 restraints weight = 40324.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.101471 restraints weight = 30555.799| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 15287 Z= 0.314 Angle : 0.755 27.045 20719 Z= 0.415 Chirality : 0.041 0.167 2270 Planarity : 0.006 0.104 2589 Dihedral : 7.767 73.721 2236 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.57 (0.18), residues: 1784 helix: -0.45 (0.17), residues: 793 sheet: -0.77 (0.36), residues: 196 loop : -1.66 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 125 TYR 0.059 0.003 TYR A 130 PHE 0.027 0.003 PHE B 730 TRP 0.033 0.003 TRP C 99 HIS 0.010 0.002 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.31 (15287) covalent geometry : angle 0.75461 / 0.42 (20719) hydrogen bonds : bond 0.04729 / 3.15 ( 732) hydrogen bonds : angle 5.60891 / 3.99 ( 2015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7320 (mm-30) REVERT: A 360 MET cc_start: 0.8439 (mtm) cc_final: 0.7526 (mtm) REVERT: A 694 LEU cc_start: 0.8728 (mt) cc_final: 0.8407 (mp) REVERT: B 243 THR cc_start: 0.9454 (m) cc_final: 0.9144 (t) REVERT: B 260 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8933 (ttp80) REVERT: B 407 MET cc_start: 0.8832 (mmm) cc_final: 0.8616 (mmm) REVERT: B 507 MET cc_start: 0.7908 (mmm) cc_final: 0.7381 (mmp) REVERT: B 690 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8122 (tm-30) REVERT: B 696 PHE cc_start: 0.8701 (t80) cc_final: 0.8458 (t80) REVERT: B 718 MET cc_start: 0.9082 (mtp) cc_final: 0.8698 (mtp) REVERT: C 11 MET cc_start: 0.8359 (mmm) cc_final: 0.8150 (mmt) REVERT: C 42 ASN cc_start: 0.8739 (t0) cc_final: 0.8257 (t0) REVERT: C 50 MET cc_start: 0.8223 (tpp) cc_final: 0.8002 (tpp) REVERT: C 212 VAL cc_start: 0.8908 (t) cc_final: 0.8683 (p) REVERT: F 83 MET cc_start: 0.8407 (mpp) cc_final: 0.7964 (mpp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2302 time to fit residues: 81.0207 Evaluate side-chains 190 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 39 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS B 641 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.114566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.092642 restraints weight = 177155.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.097256 restraints weight = 89418.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100352 restraints weight = 53832.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.102464 restraints weight = 36781.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103826 restraints weight = 27521.261| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15287 Z= 0.144 Angle : 0.574 26.577 20719 Z= 0.303 Chirality : 0.038 0.172 2270 Planarity : 0.005 0.063 2589 Dihedral : 7.476 76.768 2236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.02 (0.19), residues: 1784 helix: 0.21 (0.17), residues: 800 sheet: -0.63 (0.37), residues: 195 loop : -1.59 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.038 0.002 TYR B 82 PHE 0.024 0.002 PHE B 730 TRP 0.036 0.002 TRP C 99 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15287) covalent geometry : angle 0.57436 / 0.30 (20719) hydrogen bonds : bond 0.03974 / 2.63 ( 732) hydrogen bonds : angle 4.90815 / 3.46 ( 2015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 241 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6514 (ttt) cc_final: 0.5816 (ttm) REVERT: A 276 CYS cc_start: 0.7761 (m) cc_final: 0.7545 (m) REVERT: A 285 MET cc_start: 0.8339 (tmm) cc_final: 0.8106 (tmm) REVERT: A 344 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7239 (mm-30) REVERT: A 485 MET cc_start: 0.7399 (mtm) cc_final: 0.7173 (mtt) REVERT: A 694 LEU cc_start: 0.8695 (mt) cc_final: 0.8437 (mp) REVERT: B 174 MET cc_start: 0.5352 (ttp) cc_final: 0.4864 (ttm) REVERT: B 507 MET cc_start: 0.7408 (mmm) cc_final: 0.6701 (mmp) REVERT: B 690 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8084 (tm-30) REVERT: B 718 MET cc_start: 0.9087 (mtp) cc_final: 0.8696 (mtp) REVERT: C 7 LEU cc_start: 0.8868 (tt) cc_final: 0.8641 (tt) REVERT: C 34 TYR cc_start: 0.7397 (t80) cc_final: 0.6805 (t80) REVERT: C 42 ASN cc_start: 0.8598 (t0) cc_final: 0.8075 (t0) REVERT: C 50 MET cc_start: 0.7898 (tpp) cc_final: 0.7657 (tpp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2234 time to fit residues: 83.3012 Evaluate side-chains 196 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 113 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.113677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.092140 restraints weight = 177360.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096603 restraints weight = 90327.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.099584 restraints weight = 54741.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.101590 restraints weight = 37640.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.102869 restraints weight = 28485.364| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15287 Z= 0.133 Angle : 0.560 27.715 20719 Z= 0.293 Chirality : 0.038 0.156 2270 Planarity : 0.004 0.056 2589 Dihedral : 7.315 78.433 2236 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1784 helix: 0.53 (0.18), residues: 799 sheet: -0.47 (0.39), residues: 181 loop : -1.52 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.024 0.001 TYR B 82 PHE 0.022 0.001 PHE B 730 TRP 0.015 0.001 TRP C 99 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15287) covalent geometry : angle 0.55986 / 0.29 (20719) hydrogen bonds : bond 0.03767 / 2.51 ( 732) hydrogen bonds : angle 4.73421 / 3.35 ( 2015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6653 (ttt) cc_final: 0.6161 (ttm) REVERT: A 214 LEU cc_start: 0.8747 (mt) cc_final: 0.8546 (mt) REVERT: A 285 MET cc_start: 0.8324 (tmm) cc_final: 0.8085 (tmm) REVERT: A 483 ILE cc_start: 0.9090 (mm) cc_final: 0.8502 (tp) REVERT: A 485 MET cc_start: 0.7540 (mtm) cc_final: 0.7281 (mtt) REVERT: A 694 LEU cc_start: 0.8743 (mt) cc_final: 0.8501 (mp) REVERT: B 233 ARG cc_start: 0.7150 (mtt-85) cc_final: 0.5834 (mtt-85) REVERT: B 243 THR cc_start: 0.9487 (m) cc_final: 0.9097 (t) REVERT: B 407 MET cc_start: 0.8439 (mmm) cc_final: 0.6844 (tpp) REVERT: B 491 GLU cc_start: 0.7564 (pp20) cc_final: 0.7154 (pp20) REVERT: B 507 MET cc_start: 0.7403 (mmm) cc_final: 0.7200 (mmm) REVERT: B 690 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8194 (tm-30) REVERT: B 718 MET cc_start: 0.9230 (mtp) cc_final: 0.8848 (mtp) REVERT: C 7 LEU cc_start: 0.8935 (tt) cc_final: 0.8689 (tt) REVERT: C 90 MET cc_start: 0.6760 (ptp) cc_final: 0.6284 (ptp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2206 time to fit residues: 81.2892 Evaluate side-chains 192 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 75 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.107643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.086535 restraints weight = 185992.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090693 restraints weight = 96492.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.093500 restraints weight = 59529.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.095395 restraints weight = 41496.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096666 restraints weight = 31826.725| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15287 Z= 0.221 Angle : 0.668 26.655 20719 Z= 0.361 Chirality : 0.040 0.201 2270 Planarity : 0.005 0.074 2589 Dihedral : 7.709 83.355 2236 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.31 (0.19), residues: 1784 helix: -0.04 (0.17), residues: 805 sheet: -0.72 (0.37), residues: 196 loop : -1.75 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 716 TYR 0.028 0.002 TYR B 82 PHE 0.026 0.002 PHE B 730 TRP 0.028 0.003 TRP C 99 HIS 0.009 0.002 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (15287) covalent geometry : angle 0.66808 / 0.36 (20719) hydrogen bonds : bond 0.04258 / 2.87 ( 732) hydrogen bonds : angle 5.20836 / 3.70 ( 2015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 224 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9089 (mt) cc_final: 0.8889 (mt) REVERT: A 483 ILE cc_start: 0.9059 (mm) cc_final: 0.8529 (tp) REVERT: A 485 MET cc_start: 0.7432 (mtm) cc_final: 0.7126 (mtt) REVERT: A 597 GLU cc_start: 0.8858 (pt0) cc_final: 0.8466 (pp20) REVERT: B 243 THR cc_start: 0.9469 (m) cc_final: 0.9267 (t) REVERT: B 279 LYS cc_start: 0.7941 (mttt) cc_final: 0.7138 (pttp) REVERT: B 491 GLU cc_start: 0.7711 (pp20) cc_final: 0.7169 (pp20) REVERT: B 507 MET cc_start: 0.7519 (mmm) cc_final: 0.6774 (mmp) REVERT: B 646 MET cc_start: 0.7045 (tpt) cc_final: 0.6341 (ppp) REVERT: B 696 PHE cc_start: 0.8510 (t80) cc_final: 0.8301 (t80) REVERT: B 718 MET cc_start: 0.9347 (mtp) cc_final: 0.8879 (mtp) REVERT: C 7 LEU cc_start: 0.9045 (tt) cc_final: 0.8757 (tt) REVERT: C 42 ASN cc_start: 0.8816 (t0) cc_final: 0.8131 (t0) REVERT: F 83 MET cc_start: 0.8327 (mpp) cc_final: 0.7934 (mpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2356 time to fit residues: 82.9200 Evaluate side-chains 189 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 6 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 84 optimal weight: 0.0020 chunk 118 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.109720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088690 restraints weight = 187805.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093076 restraints weight = 95696.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096038 restraints weight = 58326.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.098030 restraints weight = 39978.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.099401 restraints weight = 30214.281| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15287 Z= 0.113 Angle : 0.568 27.109 20719 Z= 0.296 Chirality : 0.038 0.174 2270 Planarity : 0.005 0.099 2589 Dihedral : 7.425 86.140 2236 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.61 (0.18), residues: 805 sheet: -0.60 (0.37), residues: 200 loop : -1.59 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.020 0.001 TYR B 82 PHE 0.021 0.001 PHE B 730 TRP 0.018 0.002 TRP A 406 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15287) covalent geometry : angle 0.56827 / 0.30 (20719) hydrogen bonds : bond 0.03809 / 2.51 ( 732) hydrogen bonds : angle 4.67236 / 3.29 ( 2015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 227 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.765 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: A 211 MET cc_start: 0.6834 (ttt) cc_final: 0.6444 (ttm) REVERT: A 285 MET cc_start: 0.8004 (tmm) cc_final: 0.7665 (tmm) REVERT: A 483 ILE cc_start: 0.8989 (mm) cc_final: 0.8522 (tp) REVERT: A 485 MET cc_start: 0.6966 (mtm) cc_final: 0.6518 (mtt) REVERT: A 597 GLU cc_start: 0.8548 (pt0) cc_final: 0.8326 (pp20) REVERT: B 174 MET cc_start: 0.4866 (ttp) cc_final: 0.4509 (ttm) REVERT: B 179 MET cc_start: 0.6126 (mtm) cc_final: 0.5835 (mtm) REVERT: B 243 THR cc_start: 0.9526 (m) cc_final: 0.9196 (t) REVERT: B 279 LYS cc_start: 0.7737 (mttt) cc_final: 0.7018 (pptt) REVERT: B 646 MET cc_start: 0.6940 (tpt) cc_final: 0.6266 (ppp) REVERT: B 690 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8633 (tp40) REVERT: B 718 MET cc_start: 0.9359 (mtp) cc_final: 0.8900 (mtp) REVERT: C 7 LEU cc_start: 0.9026 (tt) cc_final: 0.8742 (tt) REVERT: C 42 ASN cc_start: 0.8700 (t0) cc_final: 0.8123 (t0) REVERT: C 50 MET cc_start: 0.8217 (tpp) cc_final: 0.8010 (tpp) REVERT: C 90 MET cc_start: 0.7026 (ptp) cc_final: 0.6285 (ptp) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2209 time to fit residues: 77.9468 Evaluate side-chains 190 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 70 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.105314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084656 restraints weight = 197564.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088740 restraints weight = 102711.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091467 restraints weight = 63582.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093299 restraints weight = 44584.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.094545 restraints weight = 34402.056| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.8430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15287 Z= 0.228 Angle : 0.652 27.048 20719 Z= 0.354 Chirality : 0.039 0.164 2270 Planarity : 0.005 0.063 2589 Dihedral : 7.775 87.927 2236 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.20 (0.19), residues: 1784 helix: 0.17 (0.17), residues: 809 sheet: -0.75 (0.38), residues: 196 loop : -1.83 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 663 TYR 0.021 0.002 TYR B 355 PHE 0.043 0.002 PHE A 315 TRP 0.034 0.003 TRP A 317 HIS 0.010 0.002 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (15287) covalent geometry : angle 0.65165 / 0.35 (20719) hydrogen bonds : bond 0.04219 / 2.83 ( 732) hydrogen bonds : angle 5.19999 / 3.68 ( 2015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 216 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6553 (ttt) cc_final: 0.5606 (ttm) REVERT: A 214 LEU cc_start: 0.8962 (mt) cc_final: 0.8741 (mt) REVERT: A 344 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7056 (mm-30) REVERT: A 485 MET cc_start: 0.7052 (mtm) cc_final: 0.6693 (mtt) REVERT: A 597 GLU cc_start: 0.8904 (pt0) cc_final: 0.8514 (pp20) REVERT: B 174 MET cc_start: 0.5049 (ttp) cc_final: 0.4641 (ttm) REVERT: B 243 THR cc_start: 0.9492 (m) cc_final: 0.9278 (t) REVERT: B 279 LYS cc_start: 0.7989 (mttt) cc_final: 0.7184 (pptt) REVERT: B 491 GLU cc_start: 0.7924 (pp20) cc_final: 0.7391 (pp20) REVERT: B 507 MET cc_start: 0.8078 (mmm) cc_final: 0.7648 (mmm) REVERT: B 551 PHE cc_start: 0.8715 (t80) cc_final: 0.8484 (t80) REVERT: B 645 MET cc_start: 0.7953 (mpp) cc_final: 0.7389 (mpp) REVERT: B 646 MET cc_start: 0.6988 (tpt) cc_final: 0.6252 (ppp) REVERT: B 718 MET cc_start: 0.9446 (mtp) cc_final: 0.8988 (mtp) REVERT: C 7 LEU cc_start: 0.9081 (tt) cc_final: 0.8738 (tt) REVERT: C 42 ASN cc_start: 0.8913 (t0) cc_final: 0.8269 (t0) REVERT: F 83 MET cc_start: 0.8177 (mpp) cc_final: 0.7841 (mpp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2419 time to fit residues: 81.1306 Evaluate side-chains 179 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 81 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.107911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087053 restraints weight = 190693.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.091360 restraints weight = 97776.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.094258 restraints weight = 59548.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.096198 restraints weight = 41170.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097541 restraints weight = 31302.923| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15287 Z= 0.110 Angle : 0.558 27.089 20719 Z= 0.292 Chirality : 0.038 0.164 2270 Planarity : 0.004 0.053 2589 Dihedral : 7.498 90.351 2236 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.68 (0.18), residues: 807 sheet: -0.54 (0.40), residues: 186 loop : -1.61 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 663 TYR 0.017 0.001 TYR B 82 PHE 0.021 0.001 PHE B 730 TRP 0.015 0.001 TRP A 406 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15287) covalent geometry : angle 0.55808 / 0.29 (20719) hydrogen bonds : bond 0.03766 / 2.51 ( 732) hydrogen bonds : angle 4.72430 / 3.32 ( 2015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4473.83 seconds wall clock time: 77 minutes 19.89 seconds (4639.89 seconds total)