Starting phenix.real_space_refine on Fri Mar 6 03:51:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nha_12322/03_2026/7nha_12322.map" } resolution = 2.91 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= 0.002 sd= 0.018 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 102 5.16 5 C 8854 2.51 5 N 2468 2.21 5 O 2734 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28049 Number of models: 1 Model: "" Number of chains: 5 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} Time building chain proxies: 4.22, per 1000 atoms: 0.15 Number of scatterers: 28049 At special positions: 0 Unit cell: (99, 103.95, 146.025, 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 102 16.00 P 23 15.00 O 2734 8.00 N 2468 7.00 C 8854 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 588.6 milliseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 15 sheets defined 52.1% alpha, 12.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A 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: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.777A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A 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: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.588A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.331A 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: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A 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: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A 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: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A 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: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A 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 146 692 hydrogen bonds defined for protein. 1911 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: 6.57 Time building geometry restraints manager: 3.65 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: 76 1.23 - 1.43: 6041 1.43 - 1.62: 8251 1.62 - 1.82: 177 Bond restraints: 28386 Sorted by residual: bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.23e+00 bond pdb=" CE1 PHE B 730 " pdb=" CZ PHE B 730 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CA PRO A 274 " pdb=" C PRO A 274 " ideal model delta sigma weight residual 1.514 1.520 -0.006 5.50e-03 3.31e+04 1.25e+00 bond pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" C LEU A 106 " pdb=" N PRO A 107 " ideal model delta sigma weight residual 1.326 1.340 -0.014 1.44e-02 4.82e+03 9.51e-01 ... (remaining 28381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 51274 5.64 - 11.29: 0 11.29 - 16.93: 0 16.93 - 22.58: 1 22.58 - 28.22: 5 Bond angle restraints: 51280 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 79.78 28.22 3.00e+00 1.11e-01 8.85e+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 80.33 27.67 3.00e+00 1.11e-01 8.51e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.85 27.15 3.00e+00 1.11e-01 8.19e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.45 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.75 -26.85 3.20e+00 9.77e-02 7.04e+01 ... (remaining 51275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12171 17.93 - 35.86: 828 35.86 - 53.79: 248 53.79 - 71.72: 84 71.72 - 89.65: 15 Dihedral angle restraints: 13346 sinusoidal: 7560 harmonic: 5786 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1598 0.037 - 0.074: 430 0.074 - 0.111: 101 0.111 - 0.148: 31 0.148 - 0.185: 2 Chirality restraints: 2162 Sorted by residual: chirality pdb=" CA PHE B 730 " pdb=" N PHE B 730 " pdb=" C PHE B 730 " pdb=" CB PHE B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE B 302 " pdb=" N ILE B 302 " pdb=" C ILE B 302 " pdb=" CB ILE B 302 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 2159 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 446 " -0.019 2.00e-02 2.50e+03 1.57e-02 7.42e+00 pdb=" CG PHE A 446 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 446 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 446 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 446 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 446 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 446 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 446 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 446 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 446 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 446 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 446 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 730 " 0.015 2.00e-02 2.50e+03 1.17e-02 4.08e+00 pdb=" CG PHE B 730 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 730 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 730 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE B 730 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 730 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 730 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 730 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 730 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.016 2.00e-02 2.50e+03 1.16e-02 4.05e+00 pdb=" CG PHE A 46 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 46 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 46 " 0.001 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1258 2.17 - 2.78: 56096 2.78 - 3.39: 80157 3.39 - 3.99: 104338 3.99 - 4.60: 163228 Nonbonded interactions: 405077 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 405072 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 individual isotropic 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.003 0.035 14518 Z= 0.124 Angle : 0.572 26.852 19687 Z= 0.313 Chirality : 0.038 0.185 2162 Planarity : 0.004 0.076 2456 Dihedral : 14.221 89.651 5702 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1692 helix: 0.45 (0.19), residues: 786 sheet: -0.81 (0.42), residues: 143 loop : -1.35 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 727 TYR 0.010 0.001 TYR A 24 PHE 0.048 0.002 PHE A 446 TRP 0.023 0.001 TRP A 88 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00254 (14518) covalent geometry : angle 0.57186 (19687) hydrogen bonds : bond 0.14941 ( 697) hydrogen bonds : angle 5.81236 ( 1931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 184 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 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: A 48 TYR cc_start: 0.8632 (t80) cc_final: 0.8388 (t80) REVERT: A 104 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8628 (tptt) REVERT: A 561 MET cc_start: 0.7246 (tmm) cc_final: 0.7016 (tmm) REVERT: B 743 ILE cc_start: 0.8345 (mm) cc_final: 0.7558 (mp) REVERT: C 9 ASP cc_start: 0.8742 (m-30) cc_final: 0.8531 (m-30) REVERT: C 47 MET cc_start: 0.9197 (tpp) cc_final: 0.8966 (tpp) REVERT: C 194 GLN cc_start: 0.7979 (pp30) cc_final: 0.7425 (pp30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.3379 time to fit residues: 269.0818 Evaluate side-chains 127 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 HIS B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072430 restraints weight = 89558.751| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.74 r_work: 0.3104 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14518 Z= 0.164 Angle : 0.596 27.354 19687 Z= 0.310 Chirality : 0.039 0.167 2162 Planarity : 0.005 0.074 2456 Dihedral : 10.227 73.287 2207 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.66 % Allowed : 6.88 % Favored : 92.46 % 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: -0.54 (0.20), residues: 1692 helix: 0.60 (0.19), residues: 795 sheet: -0.92 (0.41), residues: 154 loop : -1.25 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 755 TYR 0.011 0.001 TYR A 540 PHE 0.044 0.002 PHE A 446 TRP 0.010 0.001 TRP A 88 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00366 (14518) covalent geometry : angle 0.59568 (19687) hydrogen bonds : bond 0.04730 ( 697) hydrogen bonds : angle 4.84407 ( 1931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 144 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.676 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: A 48 TYR cc_start: 0.8870 (t80) cc_final: 0.8573 (t80) REVERT: B 407 MET cc_start: 0.8455 (mmm) cc_final: 0.8218 (mmm) REVERT: B 744 MET cc_start: 0.9021 (mmm) cc_final: 0.8805 (mmm) REVERT: C 9 ASP cc_start: 0.8993 (m-30) cc_final: 0.8768 (m-30) REVERT: C 194 GLN cc_start: 0.8370 (pp30) cc_final: 0.7989 (pp30) REVERT: C 195 ASP cc_start: 0.8745 (p0) cc_final: 0.8450 (p0) outliers start: 10 outliers final: 4 residues processed: 140 average time/residue: 1.1588 time to fit residues: 180.2118 Evaluate side-chains 131 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 649 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** C 73 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 = 0.3659 r_free = 0.3659 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071319 restraints weight = 89635.661| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.74 r_work: 0.3065 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14518 Z= 0.154 Angle : 0.572 26.904 19687 Z= 0.293 Chirality : 0.038 0.136 2162 Planarity : 0.004 0.049 2456 Dihedral : 10.081 73.359 2207 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.86 % Allowed : 7.81 % Favored : 91.33 % 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: -0.38 (0.20), residues: 1692 helix: 0.80 (0.19), residues: 791 sheet: -0.83 (0.41), residues: 159 loop : -1.25 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.018 0.001 TYR A 131 PHE 0.032 0.001 PHE A 446 TRP 0.007 0.001 TRP A 88 HIS 0.021 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00347 (14518) covalent geometry : angle 0.57152 (19687) hydrogen bonds : bond 0.04401 ( 697) hydrogen bonds : angle 4.62980 ( 1931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 146 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.741 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: A 48 TYR cc_start: 0.8875 (t80) cc_final: 0.8550 (t80) REVERT: A 623 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: B 744 MET cc_start: 0.8992 (mmm) cc_final: 0.8767 (mmm) REVERT: C 5 LYS cc_start: 0.8993 (tppp) cc_final: 0.8688 (tppt) REVERT: C 9 ASP cc_start: 0.9030 (m-30) cc_final: 0.8793 (m-30) REVERT: C 194 GLN cc_start: 0.8353 (pp30) cc_final: 0.7930 (pp30) REVERT: C 195 ASP cc_start: 0.8771 (p0) cc_final: 0.8425 (p0) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 1.1361 time to fit residues: 178.0209 Evaluate side-chains 134 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3645 r_free = 0.3645 target = 0.096290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070506 restraints weight = 89803.226| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.73 r_work: 0.3066 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14518 Z= 0.162 Angle : 0.569 26.281 19687 Z= 0.290 Chirality : 0.038 0.139 2162 Planarity : 0.004 0.051 2456 Dihedral : 10.028 73.437 2207 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.06 % Allowed : 8.87 % Favored : 90.07 % 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: -0.31 (0.20), residues: 1692 helix: 0.90 (0.19), residues: 793 sheet: -0.92 (0.38), residues: 176 loop : -1.24 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 116 TYR 0.012 0.001 TYR A 112 PHE 0.021 0.001 PHE A 446 TRP 0.006 0.001 TRP A 406 HIS 0.011 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00366 (14518) covalent geometry : angle 0.56871 (19687) hydrogen bonds : bond 0.04214 ( 697) hydrogen bonds : angle 4.54214 ( 1931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 150 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8845 (t80) cc_final: 0.8561 (t80) REVERT: A 88 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: A 348 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 561 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7094 (tmm) REVERT: A 623 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: B 744 MET cc_start: 0.8985 (mmm) cc_final: 0.8764 (mmm) REVERT: C 194 GLN cc_start: 0.8384 (pp30) cc_final: 0.7945 (pp30) REVERT: C 195 ASP cc_start: 0.8738 (p0) cc_final: 0.8427 (p0) outliers start: 16 outliers final: 7 residues processed: 143 average time/residue: 1.0616 time to fit residues: 169.9021 Evaluate side-chains 137 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 87 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 0.0570 chunk 168 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3627 r_free = 0.3627 target = 0.095235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069452 restraints weight = 90461.257| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.72 r_work: 0.3018 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14518 Z= 0.180 Angle : 0.578 26.938 19687 Z= 0.293 Chirality : 0.038 0.142 2162 Planarity : 0.004 0.050 2456 Dihedral : 10.015 73.505 2207 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.99 % Allowed : 9.73 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1692 helix: 0.97 (0.19), residues: 793 sheet: -1.02 (0.37), residues: 178 loop : -1.23 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.010 0.001 TYR A 112 PHE 0.020 0.001 PHE B 730 TRP 0.007 0.001 TRP A 406 HIS 0.004 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00407 (14518) covalent geometry : angle 0.57756 (19687) hydrogen bonds : bond 0.04237 ( 697) hydrogen bonds : angle 4.50041 ( 1931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 142 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8883 (t80) cc_final: 0.8549 (t80) REVERT: A 88 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: A 180 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8856 (mp-120) REVERT: A 348 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 623 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: B 744 MET cc_start: 0.8973 (mmm) cc_final: 0.8752 (mmm) REVERT: C 194 GLN cc_start: 0.8480 (pp30) cc_final: 0.8055 (pp30) REVERT: C 195 ASP cc_start: 0.8792 (p0) cc_final: 0.8476 (p0) outliers start: 15 outliers final: 6 residues processed: 135 average time/residue: 1.0782 time to fit residues: 162.6900 Evaluate side-chains 131 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3619 r_free = 0.3619 target = 0.094811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068760 restraints weight = 90718.111| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.73 r_work: 0.3028 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14518 Z= 0.184 Angle : 0.578 26.723 19687 Z= 0.293 Chirality : 0.038 0.150 2162 Planarity : 0.004 0.049 2456 Dihedral : 9.998 73.561 2207 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.79 % Allowed : 10.85 % Favored : 88.35 % 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: -0.20 (0.20), residues: 1692 helix: 1.06 (0.19), residues: 793 sheet: -1.08 (0.37), residues: 178 loop : -1.20 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.010 0.001 TYR A 110 PHE 0.022 0.001 PHE B 730 TRP 0.007 0.001 TRP A 406 HIS 0.003 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00415 (14518) covalent geometry : angle 0.57819 (19687) hydrogen bonds : bond 0.04232 ( 697) hydrogen bonds : angle 4.46516 ( 1931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 136 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.607 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: A 48 TYR cc_start: 0.8813 (t80) cc_final: 0.8464 (t80) REVERT: A 88 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: A 180 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8768 (mp-120) REVERT: A 623 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: C 194 GLN cc_start: 0.8456 (pp30) cc_final: 0.8023 (pp30) REVERT: C 195 ASP cc_start: 0.8756 (p0) cc_final: 0.8431 (p0) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 1.1217 time to fit residues: 164.2440 Evaluate side-chains 131 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3613 r_free = 0.3613 target = 0.094481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068387 restraints weight = 90353.359| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.72 r_work: 0.3021 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14518 Z= 0.176 Angle : 0.575 26.706 19687 Z= 0.291 Chirality : 0.038 0.147 2162 Planarity : 0.004 0.043 2456 Dihedral : 9.935 73.554 2207 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.93 % Allowed : 10.99 % Favored : 88.09 % 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: -0.16 (0.20), residues: 1692 helix: 1.12 (0.19), residues: 794 sheet: -1.05 (0.37), residues: 178 loop : -1.24 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.015 0.001 TYR A 110 PHE 0.021 0.001 PHE B 730 TRP 0.007 0.001 TRP A 406 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00397 (14518) covalent geometry : angle 0.57546 (19687) hydrogen bonds : bond 0.04178 ( 697) hydrogen bonds : angle 4.43060 ( 1931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 137 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.756 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: A 12 MET cc_start: 0.8725 (pp-130) cc_final: 0.8419 (pp-130) REVERT: A 48 TYR cc_start: 0.8849 (t80) cc_final: 0.8437 (t80) REVERT: A 88 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: A 348 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 623 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: B 267 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: C 195 ASP cc_start: 0.8809 (p0) cc_final: 0.8340 (p0) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 1.0879 time to fit residues: 159.2758 Evaluate side-chains 133 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 743 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 124 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3626 r_free = 0.3626 target = 0.095275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069246 restraints weight = 90139.608| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.72 r_work: 0.3026 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14518 Z= 0.126 Angle : 0.566 26.526 19687 Z= 0.281 Chirality : 0.037 0.141 2162 Planarity : 0.004 0.044 2456 Dihedral : 9.870 73.455 2207 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.86 % Allowed : 11.38 % Favored : 87.76 % 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: -0.02 (0.20), residues: 1692 helix: 1.19 (0.19), residues: 797 sheet: -0.83 (0.39), residues: 168 loop : -1.16 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.010 0.001 TYR A 110 PHE 0.027 0.001 PHE A 4 TRP 0.007 0.001 TRP A 88 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00287 (14518) covalent geometry : angle 0.56599 (19687) hydrogen bonds : bond 0.03951 ( 697) hydrogen bonds : angle 4.33673 ( 1931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 136 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.518 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: A 48 TYR cc_start: 0.8851 (t80) cc_final: 0.8471 (t80) REVERT: A 88 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: A 623 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: B 277 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8299 (mp0) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 1.0876 time to fit residues: 158.9608 Evaluate side-chains 131 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 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 = 0.3614 r_free = 0.3614 target = 0.094657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068620 restraints weight = 90325.939| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.72 r_work: 0.3017 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14518 Z= 0.151 Angle : 0.575 26.475 19687 Z= 0.287 Chirality : 0.037 0.139 2162 Planarity : 0.004 0.040 2456 Dihedral : 9.900 73.477 2207 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.93 % Allowed : 11.71 % Favored : 87.36 % 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: 0.01 (0.20), residues: 1692 helix: 1.23 (0.19), residues: 797 sheet: -0.82 (0.39), residues: 168 loop : -1.17 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.011 0.001 TYR A 110 PHE 0.019 0.001 PHE B 730 TRP 0.007 0.001 TRP A 406 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00342 (14518) covalent geometry : angle 0.57549 (19687) hydrogen bonds : bond 0.04003 ( 697) hydrogen bonds : angle 4.34392 ( 1931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 136 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.675 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: A 48 TYR cc_start: 0.8849 (t80) cc_final: 0.8423 (t80) REVERT: A 88 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: A 623 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: B 267 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: B 277 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: B 645 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7785 (mpp) REVERT: B 649 HIS cc_start: 0.7264 (m-70) cc_final: 0.6929 (m170) REVERT: C 195 ASP cc_start: 0.8678 (p0) cc_final: 0.8458 (p0) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 1.1355 time to fit residues: 166.6712 Evaluate side-chains 134 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 14 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3626 r_free = 0.3626 target = 0.095242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069320 restraints weight = 89350.091| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.71 r_work: 0.3034 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14518 Z= 0.123 Angle : 0.571 26.401 19687 Z= 0.283 Chirality : 0.037 0.139 2162 Planarity : 0.003 0.041 2456 Dihedral : 9.839 73.426 2207 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.79 % Allowed : 11.78 % Favored : 87.43 % 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: 0.15 (0.20), residues: 1692 helix: 1.34 (0.19), residues: 797 sheet: -0.71 (0.39), residues: 168 loop : -1.10 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.012 0.001 TYR A 110 PHE 0.030 0.001 PHE A 4 TRP 0.007 0.001 TRP A 88 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00281 (14518) covalent geometry : angle 0.57145 (19687) hydrogen bonds : bond 0.03831 ( 697) hydrogen bonds : angle 4.26117 ( 1931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 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 134 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.551 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: A 48 TYR cc_start: 0.8856 (t80) cc_final: 0.8421 (t80) REVERT: A 86 MET cc_start: 0.8751 (mmm) cc_final: 0.8263 (tpt) REVERT: A 88 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: A 623 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 267 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: B 277 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: B 649 HIS cc_start: 0.7273 (m-70) cc_final: 0.6955 (m170) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 1.1051 time to fit residues: 160.5000 Evaluate side-chains 134 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 88 optimal weight: 0.0570 chunk 145 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3627 r_free = 0.3627 target = 0.095479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069560 restraints weight = 89691.273| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.72 r_work: 0.3034 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 14518 Z= 0.223 Angle : 0.824 59.289 19687 Z= 0.458 Chirality : 0.037 0.315 2162 Planarity : 0.004 0.086 2456 Dihedral : 9.841 73.415 2207 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.79 % Allowed : 11.91 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1692 helix: 1.35 (0.19), residues: 797 sheet: -0.70 (0.39), residues: 168 loop : -1.10 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 727 TYR 0.010 0.001 TYR A 112 PHE 0.157 0.002 PHE A 117 TRP 0.007 0.001 TRP A 88 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00492 (14518) covalent geometry : angle 0.82412 (19687) hydrogen bonds : bond 0.03837 ( 697) hydrogen bonds : angle 4.25499 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8370.97 seconds wall clock time: 142 minutes 16.11 seconds (8536.11 seconds total)