Starting phenix.real_space_refine on Sun Jul 5 15:40:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.map" model { file = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nj3_12371/07_2026/7nj3_12371.cif" } resolution = 4.48 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= 0.011 sd= 0.138 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 105 5.16 5 C 9307 2.51 5 N 2596 2.21 5 O 2879 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: 28778 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: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 729 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 3 Time building chain proxies: 4.59, per 1000 atoms: 0.16 Number of scatterers: 28778 At special positions: 0 Unit cell: (100.1, 105.6, 159.5, 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 105 16.00 P 23 15.00 O 2879 8.00 N 2596 7.00 C 9307 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.02 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: 2.80 Conformation dependent library (CDL) restraints added in 831.2 milliseconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 17 sheets defined 49.6% alpha, 14.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.139A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.692A 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: 3.794A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.634A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.971A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.827A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.509A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.617A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.331A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.236A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.584A 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 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A 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: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.174A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.809A 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: 5.616A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 13 removed outlier: 5.836A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 164 1.23 - 1.43: 6283 1.43 - 1.62: 8656 1.62 - 1.82: 181 Bond restraints: 29125 Sorted by residual: bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.519 -0.061 1.40e-02 5.10e+03 1.90e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" CD ARG F 98 " pdb=" NE ARG F 98 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA ARG F 71 " pdb=" C ARG F 71 " ideal model delta sigma weight residual 1.521 1.487 0.034 1.24e-02 6.50e+03 7.71e+00 ... (remaining 29120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 52261 5.64 - 11.28: 7 11.28 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 Bond angle restraints: 52274 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 80.30 27.70 3.00e+00 1.11e-01 8.53e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.82 27.18 3.00e+00 1.11e-01 8.21e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.46 26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.75 -26.85 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12520 17.94 - 35.88: 849 35.88 - 53.81: 241 53.81 - 71.75: 69 71.75 - 89.69: 10 Dihedral angle restraints: 13689 sinusoidal: 7638 harmonic: 6051 Sorted by residual: dihedral pdb=" N SER F 84 " pdb=" C SER F 84 " pdb=" CA SER F 84 " pdb=" CB SER F 84 " ideal model delta harmonic sigma weight residual 122.80 136.30 -13.50 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C SER F 84 " pdb=" N SER F 84 " pdb=" CA SER F 84 " pdb=" CB SER F 84 " ideal model delta harmonic sigma weight residual -122.60 -134.28 11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 13686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2180 0.099 - 0.199: 81 0.199 - 0.298: 4 0.298 - 0.397: 3 0.397 - 0.497: 1 Chirality restraints: 2269 Sorted by residual: chirality pdb=" CA SER F 84 " pdb=" N SER F 84 " pdb=" C SER F 84 " pdb=" CB SER F 84 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA THR F 24 " pdb=" N THR F 24 " pdb=" C THR F 24 " pdb=" CB THR F 24 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS F 64 " pdb=" N LYS F 64 " pdb=" C LYS F 64 " pdb=" CB LYS F 64 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2266 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.023 2.00e-02 2.50e+03 5.44e-02 5.92e+01 pdb=" CG TYR F 32 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.088 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " 0.084 2.00e-02 2.50e+03 4.40e-02 4.84e+01 pdb=" CG TRP F 112 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 59 " 0.027 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR F 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR F 59 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 59 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 59 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR F 59 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR F 59 " 0.046 2.00e-02 2.50e+03 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1259 2.17 - 2.78: 56211 2.78 - 3.39: 80883 3.39 - 3.99: 105788 3.99 - 4.60: 165140 Nonbonded interactions: 409281 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3593 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 0.061 15258 Z= 0.242 Angle : 0.703 26.846 20683 Z= 0.412 Chirality : 0.045 0.497 2269 Planarity : 0.005 0.076 2584 Dihedral : 13.635 89.690 5883 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.38 % Allowed : 0.44 % Favored : 99.18 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1779 helix: 0.45 (0.19), residues: 786 sheet: -0.88 (0.35), residues: 193 loop : -1.29 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 71 TYR 0.088 0.003 TYR F 32 PHE 0.048 0.002 PHE A 446 TRP 0.084 0.002 TRP F 112 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.24 (15257) covalent geometry : angle 0.70155 / 0.41 (20681) SS BOND : bond 0.01513 / 0.72 ( 1) SS BOND : angle 5.12647 / 2.88 ( 2) hydrogen bonds : bond 0.15011 / 9.83 ( 731) hydrogen bonds : angle 5.85968 / 4.21 ( 2009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 422 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 416 time to evaluate : 0.701 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: A 182 MET cc_start: 0.1885 (mpp) cc_final: 0.1209 (mmt) REVERT: B 248 ILE cc_start: 0.7981 (tt) cc_final: 0.7502 (tt) REVERT: B 317 MET cc_start: 0.7206 (mmm) cc_final: 0.6531 (mmm) REVERT: C 232 LEU cc_start: 0.6244 (tp) cc_final: 0.5476 (tt) REVERT: C 243 MET cc_start: -0.1972 (mtt) cc_final: -0.3321 (tmm) REVERT: F 32 TYR cc_start: 0.3678 (m-80) cc_final: 0.3444 (p90) REVERT: F 59 TYR cc_start: 0.5504 (m-80) cc_final: 0.4920 (m-80) outliers start: 6 outliers final: 0 residues processed: 419 average time/residue: 0.3486 time to fit residues: 202.6074 Evaluate side-chains 273 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 HIS ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 310 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.212115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.165995 restraints weight = 102852.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.173375 restraints weight = 51516.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.178177 restraints weight = 31868.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.181273 restraints weight = 23129.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.182897 restraints weight = 18882.251| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15258 Z= 0.251 Angle : 0.755 27.554 20683 Z= 0.404 Chirality : 0.043 0.203 2269 Planarity : 0.006 0.064 2584 Dihedral : 7.151 64.412 2232 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.53 % 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: -1.09 (0.19), residues: 1779 helix: -0.01 (0.17), residues: 793 sheet: -0.77 (0.36), residues: 188 loop : -1.38 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 170 TYR 0.020 0.002 TYR F 58 PHE 0.027 0.003 PHE F 47 TRP 0.019 0.002 TRP A 577 HIS 0.010 0.002 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (15257) covalent geometry : angle 0.75489 / 0.40 (20681) SS BOND : bond 0.00203 / 0.10 ( 1) SS BOND : angle 1.40176 / 0.79 ( 2) hydrogen bonds : bond 0.05736 / 3.72 ( 731) hydrogen bonds : angle 5.42111 / 3.88 ( 2009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 319 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 258 GLU cc_start: 0.7174 (tp30) cc_final: 0.6642 (tp30) REVERT: A 272 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7388 (p0) REVERT: A 628 VAL cc_start: 0.6134 (t) cc_final: 0.5899 (t) REVERT: B 248 ILE cc_start: 0.9045 (tt) cc_final: 0.8723 (mm) REVERT: B 381 PHE cc_start: 0.6642 (m-80) cc_final: 0.6401 (m-80) REVERT: B 407 MET cc_start: 0.7210 (tpp) cc_final: 0.6465 (mmm) REVERT: B 408 MET cc_start: 0.6224 (tpt) cc_final: 0.4733 (tpt) REVERT: C 243 MET cc_start: -0.2076 (mtt) cc_final: -0.3103 (tmm) REVERT: F 98 ARG cc_start: 0.2061 (mmt180) cc_final: 0.1856 (mmt180) outliers start: 2 outliers final: 1 residues processed: 318 average time/residue: 0.3149 time to fit residues: 142.8060 Evaluate side-chains 260 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 GLN B 425 ASN B 460 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.212335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.167930 restraints weight = 99109.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.174968 restraints weight = 51058.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.179634 restraints weight = 31999.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.182787 restraints weight = 23285.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.184708 restraints weight = 18821.859| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15258 Z= 0.149 Angle : 0.584 26.069 20683 Z= 0.310 Chirality : 0.038 0.182 2269 Planarity : 0.004 0.051 2584 Dihedral : 6.814 67.753 2232 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -0.79 (0.19), residues: 1779 helix: 0.36 (0.18), residues: 791 sheet: -0.79 (0.34), residues: 221 loop : -1.33 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 716 TYR 0.013 0.002 TYR A 650 PHE 0.021 0.002 PHE B 574 TRP 0.018 0.001 TRP A 422 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (15257) covalent geometry : angle 0.58380 / 0.31 (20681) SS BOND : bond 0.00052 / 0.02 ( 1) SS BOND : angle 0.75356 / 0.41 ( 2) hydrogen bonds : bond 0.04683 / 3.03 ( 731) hydrogen bonds : angle 4.98070 / 3.55 ( 2009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.823 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: A 47 MET cc_start: 0.1324 (tpt) cc_final: 0.0676 (ptt) REVERT: A 258 GLU cc_start: 0.7132 (tp30) cc_final: 0.6795 (tp30) REVERT: A 272 ASP cc_start: 0.8253 (m-30) cc_final: 0.7847 (p0) REVERT: A 431 ASP cc_start: 0.7447 (p0) cc_final: 0.7201 (p0) REVERT: A 486 ILE cc_start: 0.8504 (mm) cc_final: 0.8282 (mm) REVERT: B 248 ILE cc_start: 0.8927 (tt) cc_final: 0.8605 (mm) REVERT: C 243 MET cc_start: -0.1912 (mtt) cc_final: -0.2982 (tmm) REVERT: F 98 ARG cc_start: 0.2058 (mmt180) cc_final: 0.1801 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3094 time to fit residues: 133.2080 Evaluate side-chains 254 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN B 292 ASN B 294 GLN B 328 ASN B 346 ASN B 425 ASN B 460 GLN B 605 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.200615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.153391 restraints weight = 101510.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.160035 restraints weight = 51137.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.164286 restraints weight = 32399.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.167059 restraints weight = 24133.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.168527 restraints weight = 20091.959| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15258 Z= 0.243 Angle : 0.724 28.370 20683 Z= 0.388 Chirality : 0.042 0.201 2269 Planarity : 0.007 0.142 2584 Dihedral : 7.240 75.335 2232 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % 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: -1.38 (0.18), residues: 1779 helix: -0.12 (0.17), residues: 811 sheet: -1.05 (0.34), residues: 216 loop : -1.71 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 124 TYR 0.031 0.002 TYR A 650 PHE 0.037 0.003 PHE B 381 TRP 0.016 0.002 TRP A 577 HIS 0.010 0.002 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (15257) covalent geometry : angle 0.72423 / 0.39 (20681) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.50667 / 0.27 ( 2) hydrogen bonds : bond 0.05601 / 3.64 ( 731) hydrogen bonds : angle 5.45044 / 3.87 ( 2009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 286 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.791 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: A 47 MET cc_start: 0.1460 (tpt) cc_final: 0.0890 (ptt) REVERT: A 390 LEU cc_start: 0.7962 (tp) cc_final: 0.7698 (tt) REVERT: A 453 CYS cc_start: 0.7876 (t) cc_final: 0.7664 (m) REVERT: A 486 ILE cc_start: 0.8592 (mm) cc_final: 0.8316 (mm) REVERT: B 317 MET cc_start: 0.7546 (mmm) cc_final: 0.7331 (mmt) REVERT: B 333 PHE cc_start: 0.7378 (t80) cc_final: 0.7163 (t80) REVERT: B 408 MET cc_start: 0.6343 (tpt) cc_final: 0.5957 (tpt) REVERT: B 411 MET cc_start: 0.8434 (mmm) cc_final: 0.8117 (mmm) REVERT: B 481 LYS cc_start: 0.8932 (mttm) cc_final: 0.8391 (tppt) REVERT: C 243 MET cc_start: -0.1312 (mtt) cc_final: -0.2499 (tmm) REVERT: F 18 LEU cc_start: 0.8931 (tp) cc_final: 0.8694 (tt) REVERT: F 86 LYS cc_start: 0.6934 (mttt) cc_final: 0.6561 (mmtp) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.3061 time to fit residues: 126.9281 Evaluate side-chains 238 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 88 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.202071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.156478 restraints weight = 100589.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.162909 restraints weight = 51318.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.166926 restraints weight = 32698.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.169749 restraints weight = 24658.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.171282 restraints weight = 20541.522| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15258 Z= 0.152 Angle : 0.589 25.195 20683 Z= 0.314 Chirality : 0.039 0.157 2269 Planarity : 0.005 0.060 2584 Dihedral : 7.025 78.635 2232 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -0.97 (0.19), residues: 1779 helix: 0.35 (0.18), residues: 808 sheet: -0.86 (0.36), residues: 207 loop : -1.64 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 116 TYR 0.016 0.002 TYR B 599 PHE 0.017 0.002 PHE A 520 TRP 0.012 0.001 TRP A 577 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15257) covalent geometry : angle 0.58862 / 0.31 (20681) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.60176 / 0.32 ( 2) hydrogen bonds : bond 0.04686 / 3.03 ( 731) hydrogen bonds : angle 5.08232 / 3.64 ( 2009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 289 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4771 (ptm) cc_final: 0.4050 (ppp) REVERT: A 374 MET cc_start: 0.7968 (mmm) cc_final: 0.7697 (mmm) REVERT: A 431 ASP cc_start: 0.7476 (p0) cc_final: 0.7272 (p0) REVERT: A 567 THR cc_start: 0.8576 (m) cc_final: 0.8373 (p) REVERT: B 411 MET cc_start: 0.8373 (mmm) cc_final: 0.7911 (mmm) REVERT: B 414 MET cc_start: 0.8055 (mmm) cc_final: 0.7578 (mtt) REVERT: B 460 GLN cc_start: 0.5900 (tt0) cc_final: 0.5549 (tt0) REVERT: B 534 MET cc_start: 0.4062 (tpt) cc_final: 0.3855 (tpt) REVERT: C 243 MET cc_start: -0.1370 (mtt) cc_final: -0.2488 (tmm) REVERT: F 86 LYS cc_start: 0.6918 (mttt) cc_final: 0.6535 (mmtp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3212 time to fit residues: 133.0250 Evaluate side-chains 243 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 25 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.195310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.148029 restraints weight = 103607.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.154501 restraints weight = 52146.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158771 restraints weight = 33185.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.161462 restraints weight = 24854.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.162845 restraints weight = 20842.949| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15258 Z= 0.210 Angle : 0.652 28.710 20683 Z= 0.348 Chirality : 0.039 0.165 2269 Planarity : 0.006 0.100 2584 Dihedral : 7.197 85.927 2232 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -1.27 (0.19), residues: 1779 helix: 0.15 (0.17), residues: 811 sheet: -1.17 (0.36), residues: 212 loop : -1.82 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 350 TYR 0.021 0.002 TYR A 650 PHE 0.023 0.002 PHE A 411 TRP 0.020 0.002 TRP A 317 HIS 0.011 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (15257) covalent geometry : angle 0.65150 / 0.35 (20681) SS BOND : bond 0.00342 / 0.16 ( 1) SS BOND : angle 1.41677 / 0.76 ( 2) hydrogen bonds : bond 0.05202 / 3.35 ( 731) hydrogen bonds : angle 5.32979 / 3.81 ( 2009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 279 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.772 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: A 374 MET cc_start: 0.8000 (mmm) cc_final: 0.7759 (mmm) REVERT: A 499 ASN cc_start: 0.7638 (m-40) cc_final: 0.7307 (m-40) REVERT: B 408 MET cc_start: 0.6246 (tpt) cc_final: 0.6018 (tpt) REVERT: B 411 MET cc_start: 0.8655 (mmm) cc_final: 0.7948 (mmm) REVERT: B 460 GLN cc_start: 0.6566 (tt0) cc_final: 0.6257 (tt0) REVERT: B 478 SER cc_start: 0.8465 (t) cc_final: 0.8253 (t) REVERT: B 621 GLN cc_start: 0.7758 (tt0) cc_final: 0.7479 (tt0) REVERT: C 243 MET cc_start: -0.0952 (mtt) cc_final: -0.2144 (tmm) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3167 time to fit residues: 127.4382 Evaluate side-chains 239 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 151 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN B 537 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.192187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.145075 restraints weight = 103564.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151182 restraints weight = 53593.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.155153 restraints weight = 34955.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.157702 restraints weight = 26669.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.159165 restraints weight = 22596.265| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15258 Z= 0.210 Angle : 0.652 25.839 20683 Z= 0.352 Chirality : 0.039 0.155 2269 Planarity : 0.006 0.100 2584 Dihedral : 7.335 91.627 2232 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -1.38 (0.19), residues: 1779 helix: 0.09 (0.18), residues: 807 sheet: -1.25 (0.35), residues: 214 loop : -1.88 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.020 0.002 TYR A 650 PHE 0.024 0.002 PHE F 47 TRP 0.014 0.002 TRP A 317 HIS 0.011 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15257) covalent geometry : angle 0.65152 / 0.35 (20681) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.85978 / 0.46 ( 2) hydrogen bonds : bond 0.05179 / 3.34 ( 731) hydrogen bonds : angle 5.46071 / 3.90 ( 2009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 282 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.831 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: A 272 ASP cc_start: 0.8215 (p0) cc_final: 0.7852 (p0) REVERT: A 374 MET cc_start: 0.8165 (mmm) cc_final: 0.7877 (mmm) REVERT: A 485 MET cc_start: 0.8510 (mpp) cc_final: 0.8209 (mpp) REVERT: A 499 ASN cc_start: 0.7496 (m-40) cc_final: 0.7120 (m-40) REVERT: A 629 GLU cc_start: 0.4350 (mm-30) cc_final: 0.3598 (mp0) REVERT: A 682 ASP cc_start: 0.8231 (t0) cc_final: 0.8013 (t0) REVERT: B 66 LEU cc_start: 0.7628 (tp) cc_final: 0.7404 (tp) REVERT: B 99 HIS cc_start: 0.7286 (m-70) cc_final: 0.7062 (m-70) REVERT: B 411 MET cc_start: 0.8625 (mmm) cc_final: 0.7987 (mmm) REVERT: B 478 SER cc_start: 0.8611 (t) cc_final: 0.8377 (t) REVERT: B 481 LYS cc_start: 0.8785 (mttm) cc_final: 0.8084 (mmmm) REVERT: B 523 MET cc_start: 0.5192 (mtm) cc_final: 0.4986 (mtt) REVERT: C 51 MET cc_start: 0.7782 (mmm) cc_final: 0.7471 (mmm) REVERT: C 198 ILE cc_start: 0.6928 (mp) cc_final: 0.6606 (mm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3036 time to fit residues: 124.0224 Evaluate side-chains 240 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 170 optimal weight: 0.0370 chunk 146 optimal weight: 4.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN C 134 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.196880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153242 restraints weight = 103946.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.160528 restraints weight = 57831.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.161318 restraints weight = 34101.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.162323 restraints weight = 32439.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.162973 restraints weight = 29660.135| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15258 Z= 0.116 Angle : 0.561 27.087 20683 Z= 0.293 Chirality : 0.038 0.162 2269 Planarity : 0.005 0.071 2584 Dihedral : 7.011 94.629 2232 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.85 (0.19), residues: 1779 helix: 0.63 (0.18), residues: 808 sheet: -1.12 (0.35), residues: 216 loop : -1.70 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 46 TYR 0.014 0.002 TYR C 115 PHE 0.017 0.001 PHE B 94 TRP 0.012 0.001 TRP F 112 HIS 0.008 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15257) covalent geometry : angle 0.56105 / 0.29 (20681) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.49498 / 0.26 ( 2) hydrogen bonds : bond 0.04299 / 2.78 ( 731) hydrogen bonds : angle 4.90992 / 3.50 ( 2009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.831 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 272 ASP cc_start: 0.7990 (p0) cc_final: 0.7778 (p0) REVERT: A 374 MET cc_start: 0.8036 (mmm) cc_final: 0.7751 (mmm) REVERT: B 357 PHE cc_start: 0.6501 (m-10) cc_final: 0.6202 (m-80) REVERT: B 411 MET cc_start: 0.8502 (mmm) cc_final: 0.7932 (mmm) REVERT: B 491 GLU cc_start: 0.6797 (tt0) cc_final: 0.6461 (tt0) REVERT: B 534 MET cc_start: 0.4079 (tpt) cc_final: 0.3826 (tpt) REVERT: B 664 HIS cc_start: 0.8267 (m-70) cc_final: 0.7915 (m-70) REVERT: C 198 ILE cc_start: 0.6881 (mp) cc_final: 0.6545 (mm) REVERT: C 210 GLU cc_start: 0.7332 (tt0) cc_final: 0.6980 (tp30) REVERT: C 243 MET cc_start: -0.0412 (mtt) cc_final: -0.1606 (tmm) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2915 time to fit residues: 122.1546 Evaluate side-chains 236 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 169 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS C 137 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.190722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146119 restraints weight = 109223.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151030 restraints weight = 59092.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.154036 restraints weight = 41687.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.155589 restraints weight = 30851.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.156087 restraints weight = 26790.885| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.8131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15258 Z= 0.187 Angle : 0.616 26.614 20683 Z= 0.332 Chirality : 0.039 0.149 2269 Planarity : 0.005 0.089 2584 Dihedral : 7.259 98.435 2232 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.43 % 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: -1.10 (0.19), residues: 1779 helix: 0.34 (0.17), residues: 809 sheet: -1.10 (0.36), residues: 213 loop : -1.78 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 465 TYR 0.018 0.002 TYR A 650 PHE 0.022 0.002 PHE A 520 TRP 0.017 0.002 TRP F 112 HIS 0.008 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (15257) covalent geometry : angle 0.61630 / 0.33 (20681) SS BOND : bond 0.00268 / 0.13 ( 1) SS BOND : angle 0.82477 / 0.44 ( 2) hydrogen bonds : bond 0.04875 / 3.14 ( 731) hydrogen bonds : angle 5.22610 / 3.74 ( 2009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 274 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.774 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 272 ASP cc_start: 0.7954 (p0) cc_final: 0.7744 (p0) REVERT: A 374 MET cc_start: 0.8164 (mmm) cc_final: 0.7862 (mmm) REVERT: A 431 ASP cc_start: 0.7778 (p0) cc_final: 0.7553 (p0) REVERT: A 579 MET cc_start: 0.8384 (tmm) cc_final: 0.8100 (tmm) REVERT: A 581 MET cc_start: 0.9049 (mtt) cc_final: 0.8833 (mtt) REVERT: A 682 ASP cc_start: 0.8152 (t0) cc_final: 0.7908 (t0) REVERT: B 174 MET cc_start: 0.6318 (mmm) cc_final: 0.6080 (ttm) REVERT: B 408 MET cc_start: 0.6619 (tpt) cc_final: 0.6294 (tpp) REVERT: B 411 MET cc_start: 0.8610 (mmm) cc_final: 0.7986 (mmm) REVERT: B 534 MET cc_start: 0.4292 (tpt) cc_final: 0.4047 (tpt) REVERT: B 664 HIS cc_start: 0.8495 (m-70) cc_final: 0.8156 (m-70) REVERT: B 692 CYS cc_start: 0.8661 (m) cc_final: 0.8150 (p) REVERT: C 198 ILE cc_start: 0.7049 (mp) cc_final: 0.6771 (mm) REVERT: C 210 GLU cc_start: 0.7552 (tt0) cc_final: 0.7054 (mm-30) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2890 time to fit residues: 116.1820 Evaluate side-chains 232 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN B 460 GLN B 676 ASN C 134 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 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 = 0.4620 r_free = 0.4620 target = 0.192687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.148274 restraints weight = 107654.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152551 restraints weight = 62423.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.155915 restraints weight = 45088.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.158303 restraints weight = 31690.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.158554 restraints weight = 27100.208| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.8285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15258 Z= 0.124 Angle : 0.562 26.570 20683 Z= 0.296 Chirality : 0.038 0.150 2269 Planarity : 0.005 0.074 2584 Dihedral : 7.121 100.044 2232 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.68 % 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: -0.89 (0.19), residues: 1779 helix: 0.59 (0.18), residues: 809 sheet: -1.27 (0.36), residues: 205 loop : -1.67 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.014 0.001 TYR B 324 PHE 0.017 0.001 PHE F 47 TRP 0.019 0.001 TRP F 112 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15257) covalent geometry : angle 0.56171 / 0.30 (20681) SS BOND : bond 0.00094 / 0.04 ( 1) SS BOND : angle 0.54243 / 0.29 ( 2) hydrogen bonds : bond 0.04269 / 2.76 ( 731) hydrogen bonds : angle 4.91224 / 3.51 ( 2009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 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 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.674 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: A 272 ASP cc_start: 0.7970 (p0) cc_final: 0.7745 (p0) REVERT: A 374 MET cc_start: 0.8071 (mmm) cc_final: 0.7760 (mmm) REVERT: A 431 ASP cc_start: 0.7698 (p0) cc_final: 0.7453 (p0) REVERT: A 579 MET cc_start: 0.8337 (tmm) cc_final: 0.7522 (tmm) REVERT: A 629 GLU cc_start: 0.4438 (mm-30) cc_final: 0.3770 (mp0) REVERT: A 682 ASP cc_start: 0.8094 (t0) cc_final: 0.7856 (t0) REVERT: B 174 MET cc_start: 0.6336 (mmm) cc_final: 0.6133 (ttm) REVERT: B 305 ASP cc_start: 0.7235 (m-30) cc_final: 0.7029 (m-30) REVERT: B 408 MET cc_start: 0.6700 (tpt) cc_final: 0.6440 (tpp) REVERT: B 411 MET cc_start: 0.8528 (mmm) cc_final: 0.7836 (mmm) REVERT: B 534 MET cc_start: 0.4266 (tpt) cc_final: 0.3991 (tpt) REVERT: B 664 HIS cc_start: 0.8478 (m-70) cc_final: 0.8197 (m-70) REVERT: B 692 CYS cc_start: 0.8633 (m) cc_final: 0.8082 (p) REVERT: C 198 ILE cc_start: 0.6998 (mp) cc_final: 0.6741 (mm) REVERT: C 243 MET cc_start: -0.0518 (mtt) cc_final: -0.1661 (tmm) REVERT: F 98 ARG cc_start: 0.0845 (mmt180) cc_final: 0.0533 (mmt180) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2787 time to fit residues: 113.6761 Evaluate side-chains 240 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 73 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN F 39 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.193283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.148563 restraints weight = 110833.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153411 restraints weight = 58295.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156560 restraints weight = 42729.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.158671 restraints weight = 31112.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.159058 restraints weight = 26666.372| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15258 Z= 0.115 Angle : 0.553 26.758 20683 Z= 0.289 Chirality : 0.037 0.167 2269 Planarity : 0.004 0.070 2584 Dihedral : 7.041 100.897 2232 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.68 % 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: 1779 helix: 0.71 (0.18), residues: 809 sheet: -1.20 (0.36), residues: 202 loop : -1.65 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.014 0.001 TYR B 324 PHE 0.013 0.001 PHE F 47 TRP 0.016 0.001 TRP F 112 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (15257) covalent geometry : angle 0.55337 / 0.29 (20681) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.40842 / 0.22 ( 2) hydrogen bonds : bond 0.04090 / 2.66 ( 731) hydrogen bonds : angle 4.79314 / 3.43 ( 2009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.33 seconds wall clock time: 104 minutes 59.28 seconds (6299.28 seconds total)