Starting phenix.real_space_refine on Sun Jul 5 15:43:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.map" model { file = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nki_12440/07_2026/7nki_12440.cif" } resolution = 4.67 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= 0.014 sd= 0.191 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 107 5.16 5 C 9310 2.51 5 N 2593 2.21 5 O 2874 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: 28775 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: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 3 Time building chain proxies: 4.24, per 1000 atoms: 0.15 Number of scatterers: 28775 At special positions: 0 Unit cell: (98, 106, 180, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 23 15.00 O 2874 8.00 N 2593 7.00 C 9310 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 99 " distance=2.00 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: 2.64 Conformation dependent library (CDL) restraints added in 656.1 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.6% alpha, 14.7% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.005A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.692A 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: 4.432A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.633A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.777A 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: 5.827A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.511A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.617A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.037A 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: 4.108A 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: 3.521A 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: 3.584A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A 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: 3.618A 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 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A 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: 4.714A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A 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: 6.633A 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: 4.809A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.514A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.514A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1992 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: 8.72 Time building geometry restraints manager: 3.66 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 - 1.24: 1022 1.24 - 1.43: 5554 1.43 - 1.63: 8520 1.63 - 1.83: 185 Bond restraints: 29122 Sorted by residual: bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.40e-02 5.10e+03 6.99e+00 bond pdb=" CD ARG F 70 " pdb=" NE ARG F 70 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.41e+00 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.23e+00 bond pdb=" CA ASP F 76 " pdb=" CB ASP F 76 " ideal model delta sigma weight residual 1.528 1.562 -0.035 1.39e-02 5.18e+03 6.22e+00 bond pdb=" N GLN F 1 " pdb=" CA GLN F 1 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.90e-02 2.77e+03 6.08e+00 ... (remaining 29117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 52262 5.64 - 11.27: 3 11.27 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 Bond angle restraints: 52271 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 79.81 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.32 27.68 3.00e+00 1.11e-01 8.51e+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 81.92 27.08 3.00e+00 1.11e-01 8.15e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.47 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.82 -26.92 3.20e+00 9.77e-02 7.08e+01 ... (remaining 52266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12543 17.94 - 35.89: 840 35.89 - 53.83: 242 53.83 - 71.77: 63 71.77 - 89.72: 11 Dihedral angle restraints: 13699 sinusoidal: 7646 harmonic: 6053 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 13696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1887 0.049 - 0.099: 289 0.099 - 0.148: 79 0.148 - 0.198: 15 0.198 - 0.247: 2 Chirality restraints: 2272 Sorted by residual: chirality pdb=" CA THR F 81 " pdb=" N THR F 81 " pdb=" C THR F 81 " pdb=" CB THR F 81 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ASN F 80 " pdb=" N ASN F 80 " pdb=" C ASN F 80 " pdb=" CB ASN F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA THR F 119 " pdb=" N THR F 119 " pdb=" C THR F 119 " pdb=" CB THR F 119 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2269 not shown) Planarity restraints: 4223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 100 " -0.088 2.00e-02 2.50e+03 7.63e-02 1.16e+02 pdb=" CG TYR F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 100 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 100 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 100 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR F 100 " 0.078 2.00e-02 2.50e+03 pdb=" CZ TYR F 100 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR F 100 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 102 " 0.117 2.00e-02 2.50e+03 6.21e-02 7.71e+01 pdb=" CG TYR F 102 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 102 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR F 102 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR F 102 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 102 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR F 102 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 102 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.010 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR F 37 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.038 2.00e-02 2.50e+03 ... (remaining 4220 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1254 2.17 - 2.78: 56134 2.78 - 3.39: 80888 3.39 - 3.99: 105763 3.99 - 4.60: 165059 Nonbonded interactions: 409098 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 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 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409093 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: 0.260 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: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.980 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4076 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 0.047 15255 Z= 0.221 Angle : 0.671 26.918 20680 Z= 0.391 Chirality : 0.042 0.247 2272 Planarity : 0.006 0.125 2582 Dihedral : 13.486 89.718 5891 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1778 helix: 0.45 (0.19), residues: 786 sheet: -0.62 (0.38), residues: 177 loop : -1.21 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 70 TYR 0.152 0.004 TYR F 100 PHE 0.048 0.002 PHE A 446 TRP 0.026 0.001 TRP F 36 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.22 (15254) covalent geometry : angle 0.66958 / 0.39 (20678) SS BOND : bond 0.02818 / 1.34 ( 1) SS BOND : angle 3.80957 / 2.08 ( 2) hydrogen bonds : bond 0.14849 / 9.67 ( 731) hydrogen bonds : angle 5.98919 / 4.33 ( 2012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.805 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: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.3542 (tpt) cc_final: 0.3138 (tpp) REVERT: A 271 PRO cc_start: 0.6159 (Cg_endo) cc_final: 0.5666 (Cg_exo) REVERT: A 575 MET cc_start: 0.7817 (mtm) cc_final: 0.7509 (mtm) REVERT: A 581 MET cc_start: 0.7375 (mtp) cc_final: 0.6883 (mtp) REVERT: A 585 LEU cc_start: 0.8989 (mt) cc_final: 0.8705 (mm) REVERT: A 656 GLU cc_start: 0.6639 (mm-30) cc_final: 0.5780 (mm-30) REVERT: B 136 ASN cc_start: 0.8587 (m-40) cc_final: 0.8309 (m-40) REVERT: B 146 THR cc_start: 0.7925 (p) cc_final: 0.7711 (t) REVERT: B 344 PHE cc_start: 0.7674 (m-10) cc_final: 0.7321 (m-80) REVERT: B 413 ASN cc_start: 0.8255 (m110) cc_final: 0.7671 (p0) REVERT: B 528 THR cc_start: 0.7697 (m) cc_final: 0.6843 (p) REVERT: B 529 VAL cc_start: 0.9284 (t) cc_final: 0.8895 (p) REVERT: B 530 ILE cc_start: 0.8647 (mt) cc_final: 0.8363 (mt) REVERT: B 550 LEU cc_start: 0.7139 (mt) cc_final: 0.6881 (mt) REVERT: B 590 LEU cc_start: 0.5466 (mp) cc_final: 0.5242 (mt) REVERT: B 609 VAL cc_start: 0.4959 (t) cc_final: 0.4666 (t) REVERT: B 610 CYS cc_start: 0.7551 (m) cc_final: 0.6903 (t) REVERT: B 696 PHE cc_start: 0.7573 (t80) cc_final: 0.7224 (t80) REVERT: C 24 THR cc_start: 0.7797 (p) cc_final: 0.7500 (t) REVERT: F 88 MET cc_start: -0.1690 (mmm) cc_final: -0.3576 (mmp) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3110 time to fit residues: 173.8283 Evaluate side-chains 269 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 676 ASN B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.150895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.127019 restraints weight = 151275.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.133130 restraints weight = 79607.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.137093 restraints weight = 46764.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.139786 restraints weight = 30000.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.141567 restraints weight = 20715.001| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5238 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15255 Z= 0.168 Angle : 0.616 27.487 20680 Z= 0.330 Chirality : 0.039 0.149 2272 Planarity : 0.005 0.059 2582 Dihedral : 6.730 61.932 2231 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1778 helix: 0.33 (0.18), residues: 796 sheet: -0.81 (0.38), residues: 187 loop : -1.08 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 170 TYR 0.019 0.001 TYR B 620 PHE 0.022 0.002 PHE A 446 TRP 0.016 0.002 TRP A 338 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (15254) covalent geometry : angle 0.61573 / 0.33 (20678) SS BOND : bond 0.00461 / 0.22 ( 1) SS BOND : angle 0.96765 / 0.55 ( 2) hydrogen bonds : bond 0.04709 / 3.08 ( 731) hydrogen bonds : angle 5.06590 / 3.61 ( 2012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.719 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: A 360 MET cc_start: 0.8995 (mtp) cc_final: 0.8644 (mtp) REVERT: A 423 ILE cc_start: 0.5746 (pt) cc_final: 0.5440 (tp) REVERT: A 477 MET cc_start: 0.8916 (pmm) cc_final: 0.8541 (pmm) REVERT: A 575 MET cc_start: 0.8638 (mtm) cc_final: 0.8180 (mtm) REVERT: A 581 MET cc_start: 0.8325 (mtp) cc_final: 0.8032 (mtp) REVERT: A 682 ASP cc_start: 0.6778 (t0) cc_final: 0.6123 (t0) REVERT: A 713 HIS cc_start: 0.8498 (m-70) cc_final: 0.7826 (m-70) REVERT: B 246 MET cc_start: 0.7390 (tpp) cc_final: 0.6942 (tpp) REVERT: B 306 ASN cc_start: 0.6308 (m110) cc_final: 0.5722 (m110) REVERT: B 321 MET cc_start: 0.7234 (mtt) cc_final: 0.6731 (mtt) REVERT: B 409 MET cc_start: 0.7365 (ppp) cc_final: 0.6970 (ppp) REVERT: B 413 ASN cc_start: 0.8583 (m110) cc_final: 0.7703 (p0) REVERT: B 414 MET cc_start: 0.6566 (tpp) cc_final: 0.5912 (tpp) REVERT: B 610 CYS cc_start: 0.7424 (m) cc_final: 0.7083 (t) REVERT: B 620 TYR cc_start: 0.7223 (t80) cc_final: 0.6383 (t80) REVERT: C 1 MET cc_start: 0.5906 (mmm) cc_final: 0.4821 (mmm) REVERT: C 146 ASP cc_start: 0.8120 (p0) cc_final: 0.7198 (t0) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.3181 time to fit residues: 133.6145 Evaluate side-chains 241 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 85 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 703 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 425 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.125761 restraints weight = 153605.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.131537 restraints weight = 81838.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.135370 restraints weight = 48692.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.137879 restraints weight = 31571.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.139651 restraints weight = 22266.136| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15255 Z= 0.136 Angle : 0.571 26.180 20680 Z= 0.305 Chirality : 0.038 0.139 2272 Planarity : 0.004 0.050 2582 Dihedral : 6.611 64.224 2231 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.19), residues: 1778 helix: 0.49 (0.18), residues: 805 sheet: -0.57 (0.37), residues: 191 loop : -1.09 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.032 0.001 TYR A 232 PHE 0.019 0.002 PHE A 223 TRP 0.009 0.001 TRP A 368 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15254) covalent geometry : angle 0.57147 / 0.30 (20678) SS BOND : bond 0.00283 / 0.13 ( 1) SS BOND : angle 0.64877 / 0.37 ( 2) hydrogen bonds : bond 0.04400 / 2.88 ( 731) hydrogen bonds : angle 4.84991 / 3.45 ( 2012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.8898 (mtp) cc_final: 0.8512 (mtp) REVERT: A 423 ILE cc_start: 0.5725 (pt) cc_final: 0.5290 (tp) REVERT: A 477 MET cc_start: 0.8907 (pmm) cc_final: 0.8519 (pmm) REVERT: A 575 MET cc_start: 0.8463 (mtm) cc_final: 0.8163 (mtm) REVERT: A 682 ASP cc_start: 0.7174 (t0) cc_final: 0.6536 (t0) REVERT: A 713 HIS cc_start: 0.8216 (m-70) cc_final: 0.7551 (m-70) REVERT: B 321 MET cc_start: 0.7289 (mtt) cc_final: 0.6824 (mtt) REVERT: B 413 ASN cc_start: 0.8189 (m-40) cc_final: 0.7406 (p0) REVERT: B 560 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7401 (mpt90) REVERT: C 1 MET cc_start: 0.5640 (mmm) cc_final: 0.5300 (mmm) REVERT: C 23 THR cc_start: 0.9233 (m) cc_final: 0.9012 (p) REVERT: C 67 ILE cc_start: 0.6883 (tt) cc_final: 0.6587 (tt) REVERT: C 90 MET cc_start: 0.6235 (mpp) cc_final: 0.5908 (mpp) REVERT: C 122 VAL cc_start: 0.3610 (t) cc_final: 0.2685 (t) REVERT: C 146 ASP cc_start: 0.8099 (p0) cc_final: 0.7561 (t0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3205 time to fit residues: 124.7380 Evaluate side-chains 228 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 425 ASN B 641 ASN F 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.144318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.120119 restraints weight = 155356.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.125666 restraints weight = 83397.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.129403 restraints weight = 50322.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.131941 restraints weight = 33183.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.133717 restraints weight = 23618.440| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15255 Z= 0.159 Angle : 0.582 27.455 20680 Z= 0.312 Chirality : 0.038 0.148 2272 Planarity : 0.005 0.097 2582 Dihedral : 6.682 68.344 2231 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1778 helix: 0.52 (0.18), residues: 805 sheet: -0.66 (0.35), residues: 213 loop : -1.22 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 124 TYR 0.039 0.002 TYR A 232 PHE 0.017 0.001 PHE A 612 TRP 0.012 0.001 TRP C 99 HIS 0.020 0.002 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (15254) covalent geometry : angle 0.58212 / 0.31 (20678) SS BOND : bond 0.00292 / 0.14 ( 1) SS BOND : angle 0.60948 / 0.35 ( 2) hydrogen bonds : bond 0.04228 / 2.78 ( 731) hydrogen bonds : angle 4.81982 / 3.41 ( 2012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.6066 (pt) cc_final: 0.5764 (tp) REVERT: A 477 MET cc_start: 0.8988 (pmm) cc_final: 0.8563 (pmm) REVERT: A 682 ASP cc_start: 0.7913 (t0) cc_final: 0.7244 (t0) REVERT: A 713 HIS cc_start: 0.8431 (m-70) cc_final: 0.7754 (m-70) REVERT: B 313 GLN cc_start: 0.5103 (OUTLIER) cc_final: 0.4591 (mm-40) REVERT: B 321 MET cc_start: 0.7438 (mtt) cc_final: 0.6893 (mtt) REVERT: B 411 MET cc_start: 0.7996 (mmp) cc_final: 0.7496 (mmm) REVERT: B 413 ASN cc_start: 0.8338 (m-40) cc_final: 0.7324 (p0) REVERT: B 414 MET cc_start: 0.6837 (tpp) cc_final: 0.6359 (tpp) REVERT: B 560 ARG cc_start: 0.8399 (mmt-90) cc_final: 0.7420 (mpt90) REVERT: B 579 LEU cc_start: 0.7715 (tp) cc_final: 0.7489 (tp) REVERT: B 646 MET cc_start: 0.5718 (mmp) cc_final: 0.5428 (mmp) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.3083 time to fit residues: 114.6771 Evaluate side-chains 216 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 107 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 513 ASN A 670 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 313 GLN B 425 ASN B 582 GLN B 756 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.129045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.105087 restraints weight = 167362.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.109918 restraints weight = 91335.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.113218 restraints weight = 56751.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.115488 restraints weight = 38913.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.117025 restraints weight = 28948.667| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 15255 Z= 0.282 Angle : 0.790 26.225 20680 Z= 0.430 Chirality : 0.042 0.200 2272 Planarity : 0.007 0.100 2582 Dihedral : 7.448 74.251 2231 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.52 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1778 helix: -0.28 (0.17), residues: 796 sheet: -0.78 (0.38), residues: 189 loop : -1.76 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG B 151 TYR 0.035 0.003 TYR A 232 PHE 0.026 0.003 PHE A 176 TRP 0.029 0.003 TRP C 99 HIS 0.016 0.003 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 (15254) covalent geometry : angle 0.78955 / 0.43 (20678) SS BOND : bond 0.00326 / 0.16 ( 1) SS BOND : angle 0.64971 / 0.38 ( 2) hydrogen bonds : bond 0.05220 / 3.47 ( 731) hydrogen bonds : angle 5.51215 / 3.89 ( 2012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.744 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 360 MET cc_start: 0.9229 (mtp) cc_final: 0.8809 (mtp) REVERT: A 374 MET cc_start: 0.8707 (mtt) cc_final: 0.8298 (mtt) REVERT: A 410 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6115 (mt-10) REVERT: A 446 PHE cc_start: 0.8670 (m-10) cc_final: 0.8451 (m-10) REVERT: A 464 TYR cc_start: 0.7930 (t80) cc_final: 0.7681 (t80) REVERT: A 477 MET cc_start: 0.9117 (pmm) cc_final: 0.8629 (pmm) REVERT: A 682 ASP cc_start: 0.8969 (t0) cc_final: 0.8695 (t0) REVERT: A 697 ASP cc_start: 0.7798 (t0) cc_final: 0.7487 (m-30) REVERT: B 260 ARG cc_start: 0.8837 (tmt170) cc_final: 0.8237 (ptm-80) REVERT: B 321 MET cc_start: 0.7904 (mtt) cc_final: 0.7431 (mtt) REVERT: B 483 TYR cc_start: 0.6809 (p90) cc_final: 0.6607 (p90) REVERT: B 505 PHE cc_start: 0.7448 (t80) cc_final: 0.7089 (t80) REVERT: B 507 MET cc_start: 0.7759 (mmm) cc_final: 0.7477 (mmm) REVERT: B 523 MET cc_start: 0.8372 (mmm) cc_final: 0.8124 (mmm) REVERT: B 696 PHE cc_start: 0.9462 (t80) cc_final: 0.9165 (t80) REVERT: C 47 MET cc_start: 0.8322 (tpp) cc_final: 0.7610 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3005 time to fit residues: 108.7904 Evaluate side-chains 214 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 425 ASN B 452 ASN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.131746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108266 restraints weight = 163407.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113038 restraints weight = 89215.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.116277 restraints weight = 55641.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.118582 restraints weight = 38240.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120084 restraints weight = 28289.844| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15255 Z= 0.158 Angle : 0.609 26.143 20680 Z= 0.328 Chirality : 0.038 0.147 2272 Planarity : 0.005 0.075 2582 Dihedral : 7.108 75.954 2231 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1778 helix: 0.19 (0.17), residues: 797 sheet: -0.84 (0.37), residues: 198 loop : -1.60 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 151 TYR 0.039 0.002 TYR A 232 PHE 0.023 0.002 PHE A 236 TRP 0.013 0.001 TRP B 580 HIS 0.008 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (15254) covalent geometry : angle 0.60905 / 0.33 (20678) SS BOND : bond 0.00088 / 0.04 ( 1) SS BOND : angle 0.38715 / 0.23 ( 2) hydrogen bonds : bond 0.04306 / 2.87 ( 731) hydrogen bonds : angle 5.04262 / 3.58 ( 2012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.6650 (m-80) cc_final: 0.6335 (t80) REVERT: A 86 MET cc_start: 0.8738 (tpp) cc_final: 0.8514 (mmm) REVERT: A 464 TYR cc_start: 0.8017 (t80) cc_final: 0.7773 (t80) REVERT: A 477 MET cc_start: 0.9039 (pmm) cc_final: 0.8549 (pmm) REVERT: A 697 ASP cc_start: 0.7648 (t0) cc_final: 0.7437 (m-30) REVERT: B 229 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8447 (ttmm) REVERT: B 260 ARG cc_start: 0.8795 (tmt170) cc_final: 0.8165 (ptm-80) REVERT: B 321 MET cc_start: 0.7799 (mtt) cc_final: 0.7210 (mtt) REVERT: B 412 PHE cc_start: 0.7874 (m-10) cc_final: 0.7626 (m-10) REVERT: B 414 MET cc_start: 0.6909 (tpp) cc_final: 0.6679 (tpp) REVERT: B 507 MET cc_start: 0.7917 (mmm) cc_final: 0.7650 (mmm) REVERT: B 523 MET cc_start: 0.8285 (mmm) cc_final: 0.8039 (mmm) REVERT: B 560 ARG cc_start: 0.8588 (mmt-90) cc_final: 0.7782 (mpt90) REVERT: C 45 LEU cc_start: 0.8055 (tt) cc_final: 0.7799 (tt) REVERT: C 47 MET cc_start: 0.8101 (tpp) cc_final: 0.7525 (tpp) REVERT: C 202 MET cc_start: 0.7814 (mmm) cc_final: 0.7489 (mmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2982 time to fit residues: 105.7691 Evaluate side-chains 207 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 425 ASN ** B 634 HIS ** 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 = 0.4380 r_free = 0.4380 target = 0.132506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.108906 restraints weight = 164796.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.113743 restraints weight = 89891.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.117048 restraints weight = 55706.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.119320 restraints weight = 38192.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.120885 restraints weight = 28308.351| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15255 Z= 0.132 Angle : 0.589 27.111 20680 Z= 0.313 Chirality : 0.038 0.156 2272 Planarity : 0.005 0.068 2582 Dihedral : 6.904 77.750 2231 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1778 helix: 0.47 (0.18), residues: 799 sheet: -0.73 (0.37), residues: 198 loop : -1.45 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 706 TYR 0.038 0.002 TYR A 232 PHE 0.019 0.002 PHE B 730 TRP 0.012 0.001 TRP B 580 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15254) covalent geometry : angle 0.58934 / 0.31 (20678) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.37441 / 0.22 ( 2) hydrogen bonds : bond 0.04197 / 2.86 ( 731) hydrogen bonds : angle 4.82572 / 3.42 ( 2012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.6782 (m-80) cc_final: 0.6339 (t80) REVERT: A 86 MET cc_start: 0.8829 (tpp) cc_final: 0.8625 (mmm) REVERT: A 410 GLU cc_start: 0.6686 (mt-10) cc_final: 0.5893 (mt-10) REVERT: A 464 TYR cc_start: 0.7994 (t80) cc_final: 0.7755 (t80) REVERT: A 477 MET cc_start: 0.9022 (pmm) cc_final: 0.8533 (pmm) REVERT: A 575 MET cc_start: 0.8685 (ttm) cc_final: 0.8414 (tpp) REVERT: A 579 MET cc_start: 0.8671 (tmm) cc_final: 0.8470 (tmm) REVERT: A 682 ASP cc_start: 0.8948 (t0) cc_final: 0.8683 (t0) REVERT: B 162 ARG cc_start: 0.9309 (mtm180) cc_final: 0.8811 (ttp-110) REVERT: B 229 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8107 (ttmm) REVERT: B 260 ARG cc_start: 0.8806 (tmt170) cc_final: 0.8137 (ptm-80) REVERT: B 321 MET cc_start: 0.7629 (mtt) cc_final: 0.7154 (mtt) REVERT: B 409 MET cc_start: 0.6655 (ppp) cc_final: 0.6314 (ppp) REVERT: B 507 MET cc_start: 0.7912 (mmm) cc_final: 0.7621 (mmm) REVERT: B 523 MET cc_start: 0.8248 (mmm) cc_final: 0.8015 (mmm) REVERT: B 560 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.7133 (mpt90) REVERT: B 579 LEU cc_start: 0.7929 (tp) cc_final: 0.7723 (tp) REVERT: B 646 MET cc_start: 0.5675 (mmp) cc_final: 0.5271 (mmp) REVERT: B 744 MET cc_start: 0.3097 (mmp) cc_final: 0.2700 (mmp) REVERT: C 202 MET cc_start: 0.7825 (mmm) cc_final: 0.7498 (mmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2905 time to fit residues: 101.2867 Evaluate side-chains 210 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 634 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.128545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.104642 restraints weight = 169123.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.109392 restraints weight = 91774.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.112660 restraints weight = 57160.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.114939 restraints weight = 39455.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116525 restraints weight = 29432.116| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15255 Z= 0.163 Angle : 0.608 26.486 20680 Z= 0.326 Chirality : 0.038 0.149 2272 Planarity : 0.005 0.068 2582 Dihedral : 6.992 82.610 2231 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1778 helix: 0.41 (0.18), residues: 799 sheet: -0.72 (0.37), residues: 195 loop : -1.53 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 334 TYR 0.036 0.002 TYR B 82 PHE 0.029 0.002 PHE B 696 TRP 0.014 0.002 TRP B 580 HIS 0.011 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15254) covalent geometry : angle 0.60841 / 0.33 (20678) SS BOND : bond 0.00090 / 0.04 ( 1) SS BOND : angle 0.42517 / 0.24 ( 2) hydrogen bonds : bond 0.04139 / 2.78 ( 731) hydrogen bonds : angle 4.91860 / 3.50 ( 2012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.768 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 477 MET cc_start: 0.9037 (pmm) cc_final: 0.8505 (pmm) REVERT: A 619 TRP cc_start: 0.6378 (m-90) cc_final: 0.5842 (m-90) REVERT: A 682 ASP cc_start: 0.8661 (t0) cc_final: 0.8313 (t0) REVERT: B 260 ARG cc_start: 0.9027 (tmt170) cc_final: 0.8490 (ptm-80) REVERT: B 321 MET cc_start: 0.7772 (mtt) cc_final: 0.7285 (mtt) REVERT: B 507 MET cc_start: 0.7922 (mmm) cc_final: 0.7488 (mmm) REVERT: B 523 MET cc_start: 0.8291 (mmm) cc_final: 0.8070 (mmm) REVERT: B 560 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7549 (mpt180) REVERT: B 645 MET cc_start: 0.6502 (mmp) cc_final: 0.5997 (mmp) REVERT: B 646 MET cc_start: 0.5667 (mmp) cc_final: 0.5179 (mmp) REVERT: C 47 MET cc_start: 0.7905 (tpp) cc_final: 0.7371 (tpp) REVERT: C 49 TRP cc_start: 0.7502 (t60) cc_final: 0.6802 (t60) REVERT: C 202 MET cc_start: 0.7948 (mmm) cc_final: 0.7740 (mmm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2874 time to fit residues: 101.8144 Evaluate side-chains 213 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 425 ASN B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 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 = 0.4303 r_free = 0.4303 target = 0.125415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.102304 restraints weight = 166030.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106885 restraints weight = 90390.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.109994 restraints weight = 56545.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.112155 restraints weight = 39204.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.113634 restraints weight = 29494.191| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15255 Z= 0.171 Angle : 0.620 27.317 20680 Z= 0.334 Chirality : 0.039 0.262 2272 Planarity : 0.005 0.066 2582 Dihedral : 7.148 86.145 2231 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 1778 helix: 0.34 (0.18), residues: 801 sheet: -0.74 (0.37), residues: 195 loop : -1.66 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.030 0.002 TYR A 232 PHE 0.020 0.002 PHE B 505 TRP 0.015 0.002 TRP B 580 HIS 0.011 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (15254) covalent geometry : angle 0.61991 / 0.33 (20678) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.47620 / 0.26 ( 2) hydrogen bonds : bond 0.04229 / 2.83 ( 731) hydrogen bonds : angle 5.00504 / 3.56 ( 2012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.735 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: A 79 ILE cc_start: 0.7765 (mm) cc_final: 0.7557 (mm) REVERT: A 477 MET cc_start: 0.9005 (pmm) cc_final: 0.8571 (pmm) REVERT: A 581 MET cc_start: 0.8343 (mtm) cc_final: 0.8127 (mtm) REVERT: B 229 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8265 (ttmm) REVERT: B 260 ARG cc_start: 0.9031 (tmt170) cc_final: 0.8588 (ptm-80) REVERT: B 321 MET cc_start: 0.7855 (mtt) cc_final: 0.7363 (mtt) REVERT: B 481 LYS cc_start: 0.8745 (mttm) cc_final: 0.8165 (mtmm) REVERT: B 507 MET cc_start: 0.7961 (mmm) cc_final: 0.7549 (mmm) REVERT: B 560 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7540 (mpt180) REVERT: B 579 LEU cc_start: 0.8009 (tp) cc_final: 0.7781 (tp) REVERT: B 645 MET cc_start: 0.6530 (mmp) cc_final: 0.5993 (mmp) REVERT: B 646 MET cc_start: 0.5637 (mmp) cc_final: 0.5110 (mmp) REVERT: C 49 TRP cc_start: 0.7502 (t60) cc_final: 0.6981 (t60) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3113 time to fit residues: 108.5498 Evaluate side-chains 214 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** 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 = 0.4327 r_free = 0.4327 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.104291 restraints weight = 166158.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.108867 restraints weight = 90009.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.112010 restraints weight = 56057.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.114202 restraints weight = 38614.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115500 restraints weight = 28874.416| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15255 Z= 0.123 Angle : 0.590 27.219 20680 Z= 0.312 Chirality : 0.038 0.248 2272 Planarity : 0.005 0.069 2582 Dihedral : 7.051 87.762 2231 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1778 helix: 0.65 (0.18), residues: 799 sheet: -0.59 (0.37), residues: 195 loop : -1.48 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 443 TYR 0.029 0.002 TYR A 232 PHE 0.062 0.002 PHE A 446 TRP 0.018 0.001 TRP B 580 HIS 0.011 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15254) covalent geometry : angle 0.58957 / 0.31 (20678) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.42057 / 0.23 ( 2) hydrogen bonds : bond 0.04022 / 2.71 ( 731) hydrogen bonds : angle 4.83496 / 3.44 ( 2012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.7603 (mm) cc_final: 0.7398 (mm) REVERT: A 464 TYR cc_start: 0.8122 (t80) cc_final: 0.7865 (t80) REVERT: A 477 MET cc_start: 0.8985 (pmm) cc_final: 0.8572 (pmm) REVERT: A 581 MET cc_start: 0.8264 (mtm) cc_final: 0.8039 (mtm) REVERT: B 229 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8257 (ttmm) REVERT: B 260 ARG cc_start: 0.9096 (tmt170) cc_final: 0.8463 (ptm-80) REVERT: B 411 MET cc_start: 0.7612 (mmt) cc_final: 0.7374 (mmt) REVERT: B 481 LYS cc_start: 0.8611 (mttm) cc_final: 0.8064 (mtmm) REVERT: B 507 MET cc_start: 0.7905 (mmm) cc_final: 0.7582 (mmm) REVERT: B 560 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7599 (mpt180) REVERT: B 579 LEU cc_start: 0.7958 (tp) cc_final: 0.7742 (tp) REVERT: B 645 MET cc_start: 0.6524 (mmp) cc_final: 0.6129 (mmp) REVERT: B 646 MET cc_start: 0.5617 (mmp) cc_final: 0.5132 (mmp) REVERT: C 50 MET cc_start: 0.8237 (ptm) cc_final: 0.8033 (ptm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2806 time to fit residues: 99.4835 Evaluate side-chains 213 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** 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 = 0.4323 r_free = 0.4323 target = 0.126277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.102596 restraints weight = 169224.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.107330 restraints weight = 91009.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.110556 restraints weight = 56397.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.112787 restraints weight = 38894.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.114282 restraints weight = 29100.442| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.8011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15255 Z= 0.133 Angle : 0.592 27.058 20680 Z= 0.314 Chirality : 0.038 0.198 2272 Planarity : 0.005 0.116 2582 Dihedral : 7.065 89.552 2231 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1778 helix: 0.67 (0.18), residues: 800 sheet: -0.55 (0.37), residues: 195 loop : -1.49 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 124 TYR 0.029 0.002 TYR A 232 PHE 0.043 0.002 PHE A 446 TRP 0.017 0.001 TRP B 580 HIS 0.010 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15254) covalent geometry : angle 0.59178 / 0.31 (20678) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 0.37215 / 0.20 ( 2) hydrogen bonds : bond 0.04002 / 2.70 ( 731) hydrogen bonds : angle 4.87973 / 3.46 ( 2012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5042.90 seconds wall clock time: 86 minutes 52.45 seconds (5212.45 seconds total)