Starting phenix.real_space_refine on Mon Aug 25 15:01:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk2_12429/08_2025/7nk2_12429.map" } resolution = 4.84 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= 0.027 sd= 0.342 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 107 5.16 5 C 9311 2.51 5 N 2595 2.21 5 O 2872 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28776 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: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 727 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 3 Time building chain proxies: 4.93, per 1000 atoms: 0.17 Number of scatterers: 28776 At special positions: 0 Unit cell: (102, 134, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 23 15.00 O 2872 8.00 N 2595 7.00 C 9311 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 96 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 838.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.6% alpha, 14.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.92 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: 5.021A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.792A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.432A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A 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: 3.637A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.634A 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: 3.973A 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: 5.826A 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: 3.509A 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: 3.595A 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: 4.035A 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: 3.585A 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: 4.300A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A 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: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.686A 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: 4.610A 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: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.344A 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: 3.518A 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: 3.882A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1986 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: 6.59 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 792 1.23 - 1.43: 5751 1.43 - 1.63: 8555 1.63 - 1.83: 185 Bond restraints: 29124 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.523 -0.065 1.40e-02 5.10e+03 2.16e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.515 1.486 0.029 9.30e-03 1.16e+04 9.64e+00 bond pdb=" CD ARG F 38 " pdb=" NE ARG F 38 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.40e-02 5.10e+03 8.55e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.40e-02 5.10e+03 7.87e+00 ... (remaining 29119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52249 5.65 - 11.29: 14 11.29 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.23: 5 Bond angle restraints: 52269 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.77 28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.32 27.68 3.00e+00 1.11e-01 8.52e+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 81.91 27.09 3.00e+00 1.11e-01 8.15e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.47 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.77 -26.87 3.20e+00 9.77e-02 7.05e+01 ... (remaining 52264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12557 17.92 - 35.84: 867 35.84 - 53.76: 251 53.76 - 71.68: 90 71.68 - 89.60: 17 Dihedral angle restraints: 13782 sinusoidal: 7733 harmonic: 6049 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 138.40 -15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+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 ... (remaining 13779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2200 0.112 - 0.224: 60 0.224 - 0.336: 3 0.336 - 0.448: 2 0.448 - 0.560: 1 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2263 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 59 " 0.057 2.00e-02 2.50e+03 4.05e-02 3.28e+01 pdb=" CG TYR F 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR F 59 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 59 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 59 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR F 59 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 59 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 114 " -0.070 2.00e-02 2.50e+03 3.31e-02 2.74e+01 pdb=" CG TRP F 114 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP F 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP F 114 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 114 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 114 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 114 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP F 114 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 72 " -0.212 9.50e-02 1.11e+02 9.82e-02 1.28e+01 pdb=" NE ARG F 72 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG F 72 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG F 72 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 72 " -0.022 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56222 2.78 - 3.39: 80820 3.39 - 3.99: 105815 3.99 - 4.60: 165098 Nonbonded interactions: 409217 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 1.595 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.620 2.450 ... (remaining 409212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.200 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.980 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 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 0.065 15257 Z= 0.245 Angle : 0.732 26.871 20678 Z= 0.429 Chirality : 0.046 0.560 2266 Planarity : 0.005 0.098 2583 Dihedral : 14.374 89.602 5967 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.32 % Allowed : 0.38 % Favored : 99.31 % Cbeta Deviations : 0.12 % 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 aren not related in a simple way. whole: -0.71 (0.19), residues: 1778 helix: 0.45 (0.19), residues: 786 sheet: -0.63 (0.37), residues: 180 loop : -1.32 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG F 72 TYR 0.073 0.002 TYR F 59 PHE 0.048 0.002 PHE A 446 TRP 0.070 0.002 TRP F 114 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00439 (15256) covalent geometry : angle 0.73006 (20676) SS BOND : bond 0.01865 ( 1) SS BOND : angle 5.63692 ( 2) hydrogen bonds : bond 0.14928 ( 729) hydrogen bonds : angle 5.88797 ( 2006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 463 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: -0.8027 (mpp) cc_final: -0.8851 (mtt) REVERT: A 268 LEU cc_start: 0.7539 (mt) cc_final: 0.7326 (mp) REVERT: A 367 LYS cc_start: 0.7037 (mttp) cc_final: 0.6796 (tmtt) REVERT: A 437 HIS cc_start: 0.7692 (m90) cc_final: 0.5800 (m90) REVERT: A 453 CYS cc_start: 0.9115 (t) cc_final: 0.8914 (t) REVERT: A 489 CYS cc_start: 0.8462 (p) cc_final: 0.8249 (p) REVERT: A 644 SER cc_start: 0.8863 (m) cc_final: 0.8224 (t) REVERT: B 22 PHE cc_start: 0.6950 (m-80) cc_final: 0.5805 (m-80) REVERT: B 25 THR cc_start: 0.9254 (p) cc_final: 0.8983 (p) REVERT: B 28 PRO cc_start: 0.6716 (Cg_endo) cc_final: 0.6125 (Cg_exo) REVERT: B 43 VAL cc_start: 0.8472 (t) cc_final: 0.8256 (t) REVERT: B 92 MET cc_start: 0.7829 (mmm) cc_final: 0.6981 (mmm) REVERT: B 314 ASN cc_start: 0.8203 (t0) cc_final: 0.7679 (t0) REVERT: B 414 MET cc_start: 0.7615 (mmm) cc_final: 0.6993 (mmm) REVERT: B 485 ASN cc_start: 0.5524 (p0) cc_final: 0.4649 (p0) REVERT: B 493 THR cc_start: 0.8654 (m) cc_final: 0.8425 (p) REVERT: B 525 ILE cc_start: 0.9340 (mt) cc_final: 0.9007 (tp) REVERT: B 568 ILE cc_start: 0.8010 (mt) cc_final: 0.7786 (mt) REVERT: B 645 MET cc_start: 0.4828 (mpp) cc_final: 0.4503 (mtp) REVERT: B 721 ARG cc_start: 0.5446 (ttt-90) cc_final: 0.3436 (tpt170) REVERT: F 68 PHE cc_start: 0.7775 (m-10) cc_final: 0.6117 (m-10) outliers start: 5 outliers final: 1 residues processed: 467 average time/residue: 0.2748 time to fit residues: 182.4692 Evaluate side-chains 297 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 312 ASN B 425 ASN F 39 GLN ** F 82 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 = 0.4567 r_free = 0.4567 target = 0.196899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157781 restraints weight = 116480.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164489 restraints weight = 60508.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.167603 restraints weight = 35516.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169887 restraints weight = 25053.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170400 restraints weight = 20377.938| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15257 Z= 0.220 Angle : 0.690 27.637 20678 Z= 0.369 Chirality : 0.041 0.162 2266 Planarity : 0.005 0.059 2583 Dihedral : 10.228 73.339 2307 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % 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 aren not related in a simple way. whole: -0.90 (0.19), residues: 1778 helix: 0.19 (0.18), residues: 803 sheet: -0.77 (0.35), residues: 192 loop : -1.33 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.014 0.002 TYR A 393 PHE 0.039 0.002 PHE F 47 TRP 0.016 0.002 TRP A 338 HIS 0.009 0.002 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00468 (15256) covalent geometry : angle 0.69010 (20676) SS BOND : bond 0.00428 ( 1) SS BOND : angle 1.75387 ( 2) hydrogen bonds : bond 0.04957 ( 729) hydrogen bonds : angle 5.20427 ( 2006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.764 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 12 MET cc_start: 0.6647 (ppp) cc_final: 0.5536 (ppp) REVERT: A 284 LEU cc_start: 0.8962 (mt) cc_final: 0.8707 (mt) REVERT: A 367 LYS cc_start: 0.7228 (mttp) cc_final: 0.6830 (tttp) REVERT: A 370 LEU cc_start: 0.8563 (mt) cc_final: 0.8298 (mt) REVERT: A 410 GLU cc_start: 0.7674 (tt0) cc_final: 0.6943 (tt0) REVERT: A 477 MET cc_start: 0.7117 (ptp) cc_final: 0.6878 (ptp) REVERT: A 523 MET cc_start: 0.7772 (mtm) cc_final: 0.7511 (mtm) REVERT: A 581 MET cc_start: 0.9401 (mtp) cc_final: 0.8620 (ttm) REVERT: A 644 SER cc_start: 0.8682 (m) cc_final: 0.8400 (t) REVERT: A 682 ASP cc_start: 0.7844 (t0) cc_final: 0.7185 (t0) REVERT: A 697 ASP cc_start: 0.8640 (t0) cc_final: 0.7881 (m-30) REVERT: B 40 MET cc_start: 0.9173 (mtm) cc_final: 0.8365 (ptp) REVERT: B 78 GLU cc_start: 0.8931 (mp0) cc_final: 0.8722 (mp0) REVERT: B 256 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8468 (tp30) REVERT: B 314 ASN cc_start: 0.7540 (t0) cc_final: 0.7303 (t0) REVERT: B 321 MET cc_start: 0.6393 (mtp) cc_final: 0.5983 (mtp) REVERT: B 343 MET cc_start: 0.7039 (mtp) cc_final: 0.6814 (mtp) REVERT: B 373 LEU cc_start: 0.9373 (mt) cc_final: 0.9056 (mt) REVERT: B 409 MET cc_start: 0.8747 (tmm) cc_final: 0.8542 (tmm) REVERT: B 411 MET cc_start: 0.8098 (mpp) cc_final: 0.6828 (tpp) REVERT: B 445 ASP cc_start: 0.5828 (t0) cc_final: 0.5407 (t0) REVERT: B 543 THR cc_start: 0.8322 (m) cc_final: 0.8080 (m) REVERT: B 744 MET cc_start: 0.7510 (tpt) cc_final: 0.6984 (mmm) REVERT: C 20 LEU cc_start: 0.8696 (mt) cc_final: 0.8473 (mt) REVERT: C 90 MET cc_start: 0.3711 (ttp) cc_final: 0.2910 (tpp) REVERT: F 34 MET cc_start: 0.6220 (mmp) cc_final: 0.5867 (mmm) REVERT: F 83 MET cc_start: 0.8225 (mtt) cc_final: 0.7854 (mtm) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.2539 time to fit residues: 121.5574 Evaluate side-chains 261 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 425 ASN B 605 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4519 r_free = 0.4519 target = 0.193626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154612 restraints weight = 117444.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.160185 restraints weight = 59153.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163825 restraints weight = 35962.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.166174 restraints weight = 25388.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167040 restraints weight = 20489.320| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15257 Z= 0.156 Angle : 0.576 25.976 20678 Z= 0.306 Chirality : 0.038 0.143 2266 Planarity : 0.004 0.067 2583 Dihedral : 10.039 73.261 2307 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.19), residues: 1778 helix: 0.51 (0.18), residues: 809 sheet: -0.75 (0.35), residues: 202 loop : -1.31 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 116 TYR 0.011 0.001 TYR A 112 PHE 0.027 0.002 PHE F 47 TRP 0.014 0.002 TRP A 577 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00336 (15256) covalent geometry : angle 0.57564 (20676) SS BOND : bond 0.00113 ( 1) SS BOND : angle 1.14676 ( 2) hydrogen bonds : bond 0.04540 ( 729) hydrogen bonds : angle 4.89029 ( 2006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8475 (mt) cc_final: 0.8263 (mm) REVERT: A 249 MET cc_start: 0.7540 (ttm) cc_final: 0.7109 (ttm) REVERT: A 284 LEU cc_start: 0.8918 (mt) cc_final: 0.8509 (mt) REVERT: A 370 LEU cc_start: 0.9024 (mt) cc_final: 0.8764 (mt) REVERT: A 410 GLU cc_start: 0.7522 (tt0) cc_final: 0.7240 (tt0) REVERT: A 477 MET cc_start: 0.7544 (ptp) cc_final: 0.7198 (ptp) REVERT: A 579 MET cc_start: 0.8763 (ttm) cc_final: 0.8165 (ttm) REVERT: A 581 MET cc_start: 0.9489 (mtp) cc_final: 0.9046 (ttm) REVERT: A 682 ASP cc_start: 0.8177 (t0) cc_final: 0.7821 (t0) REVERT: A 697 ASP cc_start: 0.8916 (t0) cc_final: 0.7953 (m-30) REVERT: B 22 PHE cc_start: 0.8120 (m-80) cc_final: 0.7682 (m-80) REVERT: B 25 THR cc_start: 0.8956 (p) cc_final: 0.8522 (p) REVERT: B 67 ASN cc_start: 0.7929 (t0) cc_final: 0.7292 (m-40) REVERT: B 179 MET cc_start: 0.7024 (ttp) cc_final: 0.6001 (tmm) REVERT: B 256 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8420 (tp30) REVERT: B 267 GLU cc_start: 0.8042 (tt0) cc_final: 0.7680 (mp0) REVERT: B 314 ASN cc_start: 0.8042 (t0) cc_final: 0.7556 (t0) REVERT: B 493 THR cc_start: 0.8989 (m) cc_final: 0.8739 (p) REVERT: B 673 SER cc_start: 0.8536 (t) cc_final: 0.8242 (p) REVERT: B 744 MET cc_start: 0.7524 (tpt) cc_final: 0.7039 (mmm) REVERT: F 83 MET cc_start: 0.7715 (mtt) cc_final: 0.7243 (mtm) REVERT: F 90 ASP cc_start: 0.7928 (m-30) cc_final: 0.7678 (m-30) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2429 time to fit residues: 110.8796 Evaluate side-chains 251 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN B 284 ASN B 425 ASN B 569 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.189713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144898 restraints weight = 117627.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150160 restraints weight = 59894.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153753 restraints weight = 37832.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155979 restraints weight = 28108.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156974 restraints weight = 23433.459| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15257 Z= 0.194 Angle : 0.635 28.631 20678 Z= 0.337 Chirality : 0.040 0.303 2266 Planarity : 0.006 0.135 2583 Dihedral : 10.160 77.656 2307 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 aren not related in a simple way. whole: -0.73 (0.19), residues: 1778 helix: 0.56 (0.18), residues: 802 sheet: -0.80 (0.36), residues: 206 loop : -1.49 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 124 TYR 0.016 0.002 TYR C 118 PHE 0.018 0.002 PHE B 9 TRP 0.011 0.002 TRP A 619 HIS 0.012 0.002 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00418 (15256) covalent geometry : angle 0.63487 (20676) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.69467 ( 2) hydrogen bonds : bond 0.04557 ( 729) hydrogen bonds : angle 4.99885 ( 2006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 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: A 214 LEU cc_start: 0.8232 (mt) cc_final: 0.7860 (mm) REVERT: A 249 MET cc_start: 0.7622 (ttm) cc_final: 0.7303 (ttm) REVERT: A 446 PHE cc_start: 0.8049 (m-80) cc_final: 0.7842 (m-80) REVERT: A 477 MET cc_start: 0.7889 (ptp) cc_final: 0.7613 (ptp) REVERT: A 516 ASP cc_start: 0.6930 (m-30) cc_final: 0.6718 (m-30) REVERT: A 682 ASP cc_start: 0.8747 (t0) cc_final: 0.8406 (t0) REVERT: A 697 ASP cc_start: 0.9391 (t0) cc_final: 0.8686 (m-30) REVERT: B 22 PHE cc_start: 0.8120 (m-80) cc_final: 0.7839 (m-80) REVERT: B 25 THR cc_start: 0.8963 (p) cc_final: 0.8631 (p) REVERT: B 44 ASN cc_start: 0.8787 (m110) cc_final: 0.8543 (m-40) REVERT: B 67 ASN cc_start: 0.8154 (t0) cc_final: 0.7168 (m-40) REVERT: B 224 LEU cc_start: 0.7718 (tt) cc_final: 0.7513 (tt) REVERT: B 225 ASN cc_start: 0.8778 (t0) cc_final: 0.8161 (t0) REVERT: B 246 MET cc_start: 0.8189 (pmm) cc_final: 0.7732 (pmm) REVERT: B 267 GLU cc_start: 0.7887 (tt0) cc_final: 0.7614 (mp0) REVERT: B 493 THR cc_start: 0.8658 (m) cc_final: 0.8343 (p) REVERT: B 568 ILE cc_start: 0.8288 (mt) cc_final: 0.8026 (mt) REVERT: B 570 THR cc_start: 0.4839 (p) cc_final: 0.4453 (m) REVERT: B 673 SER cc_start: 0.8710 (t) cc_final: 0.8324 (p) REVERT: B 718 MET cc_start: 0.8537 (mtp) cc_final: 0.7884 (mmm) REVERT: B 744 MET cc_start: 0.7592 (tpt) cc_final: 0.7083 (mmm) REVERT: C 90 MET cc_start: 0.3631 (ttp) cc_final: 0.3288 (tpp) REVERT: F 83 MET cc_start: 0.8033 (mtt) cc_final: 0.7778 (mtm) REVERT: F 90 ASP cc_start: 0.8289 (m-30) cc_final: 0.7914 (m-30) REVERT: F 120 VAL cc_start: 0.8422 (t) cc_final: 0.8067 (t) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2556 time to fit residues: 112.2040 Evaluate side-chains 250 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 16 optimal weight: 50.0000 chunk 177 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS B 425 ASN B 476 ASN B 634 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4420 r_free = 0.4420 target = 0.183750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139447 restraints weight = 111602.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144841 restraints weight = 56164.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.148367 restraints weight = 34827.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150058 restraints weight = 25660.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.151733 restraints weight = 21746.539| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15257 Z= 0.131 Angle : 0.562 26.427 20678 Z= 0.292 Chirality : 0.037 0.143 2266 Planarity : 0.004 0.037 2583 Dihedral : 10.160 81.111 2307 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.19), residues: 1778 helix: 0.81 (0.18), residues: 803 sheet: -0.79 (0.35), residues: 213 loop : -1.39 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.019 0.001 TYR B 30 PHE 0.021 0.001 PHE F 47 TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00284 (15256) covalent geometry : angle 0.56199 (20676) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.52633 ( 2) hydrogen bonds : bond 0.04171 ( 729) hydrogen bonds : angle 4.76228 ( 2006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8089 (mt) cc_final: 0.7763 (mm) REVERT: A 249 MET cc_start: 0.7663 (ttm) cc_final: 0.7211 (ttm) REVERT: A 516 ASP cc_start: 0.7237 (m-30) cc_final: 0.6234 (t70) REVERT: A 676 LEU cc_start: 0.8296 (mt) cc_final: 0.7973 (mt) REVERT: A 682 ASP cc_start: 0.8830 (t0) cc_final: 0.8524 (t0) REVERT: A 697 ASP cc_start: 0.9286 (t0) cc_final: 0.8398 (m-30) REVERT: B 22 PHE cc_start: 0.8313 (m-80) cc_final: 0.7963 (m-80) REVERT: B 25 THR cc_start: 0.8846 (p) cc_final: 0.8566 (p) REVERT: B 44 ASN cc_start: 0.8751 (m110) cc_final: 0.8541 (m-40) REVERT: B 69 ILE cc_start: 0.9107 (mm) cc_final: 0.8788 (tp) REVERT: B 78 GLU cc_start: 0.9357 (mp0) cc_final: 0.9151 (mp0) REVERT: B 225 ASN cc_start: 0.8681 (t0) cc_final: 0.8287 (t0) REVERT: B 246 MET cc_start: 0.7941 (pmm) cc_final: 0.7635 (pmm) REVERT: B 256 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8558 (tp30) REVERT: B 267 GLU cc_start: 0.7813 (tt0) cc_final: 0.7566 (mp0) REVERT: B 289 MET cc_start: 0.6321 (mmt) cc_final: 0.6118 (mmt) REVERT: B 452 ASN cc_start: 0.8064 (m-40) cc_final: 0.7490 (t0) REVERT: B 459 ILE cc_start: 0.9388 (mm) cc_final: 0.9182 (mm) REVERT: B 570 THR cc_start: 0.4993 (p) cc_final: 0.4617 (m) REVERT: B 673 SER cc_start: 0.8663 (t) cc_final: 0.8314 (p) REVERT: B 744 MET cc_start: 0.7573 (tpt) cc_final: 0.7080 (mmm) REVERT: C 90 MET cc_start: 0.3872 (ttp) cc_final: 0.3462 (tpp) REVERT: F 83 MET cc_start: 0.8203 (mtt) cc_final: 0.7936 (mtt) REVERT: F 90 ASP cc_start: 0.8241 (m-30) cc_final: 0.7876 (m-30) REVERT: F 120 VAL cc_start: 0.8476 (t) cc_final: 0.8180 (t) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2468 time to fit residues: 108.5680 Evaluate side-chains 248 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 overall best weight: 2.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4302 r_free = 0.4302 target = 0.174347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129965 restraints weight = 112521.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135089 restraints weight = 56917.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138489 restraints weight = 35592.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140198 restraints weight = 26185.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141603 restraints weight = 22148.544| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15257 Z= 0.200 Angle : 0.629 25.678 20678 Z= 0.338 Chirality : 0.039 0.156 2266 Planarity : 0.005 0.048 2583 Dihedral : 10.326 88.952 2307 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 aren not related in a simple way. whole: -0.84 (0.19), residues: 1778 helix: 0.47 (0.18), residues: 815 sheet: -0.53 (0.37), residues: 192 loop : -1.68 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 116 TYR 0.027 0.002 TYR A 464 PHE 0.013 0.002 PHE B 344 TRP 0.016 0.002 TRP F 36 HIS 0.017 0.002 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00412 (15256) covalent geometry : angle 0.62859 (20676) SS BOND : bond 0.03488 ( 1) SS BOND : angle 0.01938 ( 2) hydrogen bonds : bond 0.04615 ( 729) hydrogen bonds : angle 5.07509 ( 2006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 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: A 459 ILE cc_start: 0.9486 (mm) cc_final: 0.9146 (mm) REVERT: A 516 ASP cc_start: 0.8152 (m-30) cc_final: 0.7328 (t70) REVERT: A 597 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7802 (pp20) REVERT: A 682 ASP cc_start: 0.8947 (t0) cc_final: 0.7157 (p0) REVERT: A 697 ASP cc_start: 0.9383 (t0) cc_final: 0.8357 (m-30) REVERT: A 707 PHE cc_start: 0.9327 (t80) cc_final: 0.9086 (t80) REVERT: B 22 PHE cc_start: 0.8383 (m-80) cc_final: 0.8113 (m-80) REVERT: B 25 THR cc_start: 0.8928 (p) cc_final: 0.8685 (p) REVERT: B 69 ILE cc_start: 0.9210 (mm) cc_final: 0.8988 (tp) REVERT: B 225 ASN cc_start: 0.8837 (t0) cc_final: 0.8351 (t0) REVERT: B 246 MET cc_start: 0.7985 (pmm) cc_final: 0.7644 (pmm) REVERT: B 267 GLU cc_start: 0.7939 (tt0) cc_final: 0.6856 (tm-30) REVERT: B 289 MET cc_start: 0.6678 (mmt) cc_final: 0.6131 (mmt) REVERT: B 367 GLN cc_start: 0.8071 (mt0) cc_final: 0.7730 (mt0) REVERT: B 452 ASN cc_start: 0.8195 (m-40) cc_final: 0.7601 (t0) REVERT: B 459 ILE cc_start: 0.9592 (mm) cc_final: 0.9357 (mm) REVERT: B 570 THR cc_start: 0.4522 (p) cc_final: 0.3941 (m) REVERT: B 664 HIS cc_start: 0.6853 (m90) cc_final: 0.6063 (m-70) REVERT: B 673 SER cc_start: 0.8805 (t) cc_final: 0.8434 (p) REVERT: B 744 MET cc_start: 0.7647 (tpt) cc_final: 0.7253 (mmm) REVERT: C 90 MET cc_start: 0.4614 (ttp) cc_final: 0.4028 (tpp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2296 time to fit residues: 98.9077 Evaluate side-chains 241 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4363 r_free = 0.4363 target = 0.178199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135739 restraints weight = 123874.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140227 restraints weight = 66105.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143648 restraints weight = 43244.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145456 restraints weight = 32846.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146243 restraints weight = 27891.793| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15257 Z= 0.124 Angle : 0.560 28.131 20678 Z= 0.292 Chirality : 0.037 0.150 2266 Planarity : 0.004 0.039 2583 Dihedral : 10.272 91.901 2307 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 aren not related in a simple way. whole: -0.51 (0.19), residues: 1778 helix: 0.75 (0.18), residues: 814 sheet: -0.37 (0.38), residues: 193 loop : -1.53 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.012 0.001 TYR C 118 PHE 0.013 0.001 PHE A 176 TRP 0.011 0.001 TRP A 619 HIS 0.010 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00267 (15256) covalent geometry : angle 0.55974 (20676) SS BOND : bond 0.00439 ( 1) SS BOND : angle 1.00749 ( 2) hydrogen bonds : bond 0.04175 ( 729) hydrogen bonds : angle 4.87080 ( 2006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.534 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: A 232 TYR cc_start: 0.7840 (t80) cc_final: 0.7327 (t80) REVERT: A 516 ASP cc_start: 0.8233 (m-30) cc_final: 0.7780 (t70) REVERT: A 561 MET cc_start: 0.7055 (ttt) cc_final: 0.6841 (ttt) REVERT: A 577 TRP cc_start: 0.8509 (m100) cc_final: 0.8094 (m100) REVERT: A 597 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7770 (pp20) REVERT: A 676 LEU cc_start: 0.8746 (mp) cc_final: 0.8200 (mp) REVERT: A 682 ASP cc_start: 0.8993 (t0) cc_final: 0.7262 (p0) REVERT: A 697 ASP cc_start: 0.9332 (t0) cc_final: 0.8259 (m-30) REVERT: A 707 PHE cc_start: 0.9209 (t80) cc_final: 0.8987 (t80) REVERT: B 22 PHE cc_start: 0.8288 (m-80) cc_final: 0.8004 (m-80) REVERT: B 25 THR cc_start: 0.8922 (p) cc_final: 0.8589 (p) REVERT: B 44 ASN cc_start: 0.8586 (m110) cc_final: 0.8372 (m-40) REVERT: B 92 MET cc_start: 0.9195 (mmm) cc_final: 0.8217 (mmm) REVERT: B 225 ASN cc_start: 0.8767 (t0) cc_final: 0.8368 (t0) REVERT: B 246 MET cc_start: 0.7827 (pmm) cc_final: 0.7390 (pmm) REVERT: B 267 GLU cc_start: 0.7781 (tt0) cc_final: 0.6777 (tm-30) REVERT: B 331 GLU cc_start: 0.7070 (pm20) cc_final: 0.6370 (pp20) REVERT: B 343 MET cc_start: 0.8306 (mtp) cc_final: 0.7911 (mmm) REVERT: B 362 MET cc_start: 0.7582 (mmm) cc_final: 0.7283 (mmp) REVERT: B 367 GLN cc_start: 0.7876 (mt0) cc_final: 0.7660 (mt0) REVERT: B 414 MET cc_start: 0.8895 (mmm) cc_final: 0.7967 (mmm) REVERT: B 459 ILE cc_start: 0.9510 (mm) cc_final: 0.9267 (mm) REVERT: B 673 SER cc_start: 0.8736 (t) cc_final: 0.8348 (p) REVERT: B 744 MET cc_start: 0.7668 (tpt) cc_final: 0.7301 (mmp) REVERT: C 90 MET cc_start: 0.4050 (ttp) cc_final: 0.3729 (tpp) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2187 time to fit residues: 94.5838 Evaluate side-chains 243 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4320 r_free = 0.4320 target = 0.174727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131905 restraints weight = 124881.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136504 restraints weight = 65303.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139933 restraints weight = 42564.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141872 restraints weight = 32120.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142756 restraints weight = 27306.245| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15257 Z= 0.151 Angle : 0.573 26.906 20678 Z= 0.302 Chirality : 0.038 0.238 2266 Planarity : 0.005 0.101 2583 Dihedral : 10.337 94.773 2307 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.19), residues: 1778 helix: 0.76 (0.18), residues: 815 sheet: -0.36 (0.38), residues: 193 loop : -1.53 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.019 0.002 TYR B 355 PHE 0.023 0.002 PHE B 496 TRP 0.011 0.002 TRP F 114 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00326 (15256) covalent geometry : angle 0.57269 (20676) SS BOND : bond 0.00452 ( 1) SS BOND : angle 2.14310 ( 2) hydrogen bonds : bond 0.04211 ( 729) hydrogen bonds : angle 4.90742 ( 2006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.936 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: A 232 TYR cc_start: 0.8576 (t80) cc_final: 0.7986 (t80) REVERT: A 374 MET cc_start: 0.6495 (mmp) cc_final: 0.6289 (mmm) REVERT: A 463 VAL cc_start: 0.8993 (t) cc_final: 0.8723 (p) REVERT: A 577 TRP cc_start: 0.8560 (m100) cc_final: 0.8236 (m100) REVERT: A 597 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7793 (pp20) REVERT: A 676 LEU cc_start: 0.8753 (mp) cc_final: 0.8199 (mp) REVERT: A 682 ASP cc_start: 0.9002 (t0) cc_final: 0.7826 (p0) REVERT: A 697 ASP cc_start: 0.9329 (t0) cc_final: 0.8130 (m-30) REVERT: A 707 PHE cc_start: 0.9345 (t80) cc_final: 0.9083 (t80) REVERT: B 22 PHE cc_start: 0.8404 (m-80) cc_final: 0.8140 (m-80) REVERT: B 225 ASN cc_start: 0.8841 (t0) cc_final: 0.8474 (t0) REVERT: B 227 MET cc_start: 0.8629 (tpp) cc_final: 0.8400 (tpp) REVERT: B 246 MET cc_start: 0.7812 (pmm) cc_final: 0.7383 (pmm) REVERT: B 267 GLU cc_start: 0.7840 (tt0) cc_final: 0.6695 (tm-30) REVERT: B 290 MET cc_start: 0.7315 (ttt) cc_final: 0.6434 (tpt) REVERT: B 331 GLU cc_start: 0.7155 (pm20) cc_final: 0.6406 (pp20) REVERT: B 343 MET cc_start: 0.8411 (mtp) cc_final: 0.7930 (mmm) REVERT: B 367 GLN cc_start: 0.8156 (mt0) cc_final: 0.7906 (mt0) REVERT: B 414 MET cc_start: 0.9072 (mmm) cc_final: 0.8178 (mmm) REVERT: B 664 HIS cc_start: 0.6952 (m90) cc_final: 0.6733 (m-70) REVERT: B 673 SER cc_start: 0.8718 (t) cc_final: 0.8376 (p) REVERT: B 744 MET cc_start: 0.7699 (tpt) cc_final: 0.7322 (mmp) REVERT: C 11 MET cc_start: 0.8635 (mmt) cc_final: 0.7842 (mmm) REVERT: C 90 MET cc_start: 0.4018 (ttp) cc_final: 0.3760 (tpp) REVERT: F 79 LEU cc_start: 0.7576 (tp) cc_final: 0.7323 (tp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2592 time to fit residues: 108.2464 Evaluate side-chains 237 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.0670 chunk 176 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** F 82 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 = 0.4356 r_free = 0.4356 target = 0.177177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134899 restraints weight = 123216.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139493 restraints weight = 64428.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142932 restraints weight = 41836.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.144814 restraints weight = 31749.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145624 restraints weight = 27008.008| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15257 Z= 0.105 Angle : 0.542 27.117 20678 Z= 0.279 Chirality : 0.037 0.184 2266 Planarity : 0.005 0.086 2583 Dihedral : 10.340 96.442 2307 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % 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 aren not related in a simple way. whole: -0.16 (0.20), residues: 1778 helix: 1.03 (0.18), residues: 810 sheet: -0.22 (0.37), residues: 205 loop : -1.31 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 468 TYR 0.012 0.001 TYR B 620 PHE 0.038 0.001 PHE B 496 TRP 0.011 0.001 TRP A 619 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00232 (15256) covalent geometry : angle 0.54207 (20676) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.53733 ( 2) hydrogen bonds : bond 0.03845 ( 729) hydrogen bonds : angle 4.57688 ( 2006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.799 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: A 232 TYR cc_start: 0.8551 (t80) cc_final: 0.7888 (t80) REVERT: A 249 MET cc_start: 0.7702 (ttp) cc_final: 0.7378 (ptm) REVERT: A 282 PHE cc_start: 0.8885 (p90) cc_final: 0.8536 (p90) REVERT: A 437 HIS cc_start: 0.8478 (t70) cc_final: 0.8177 (m-70) REVERT: A 577 TRP cc_start: 0.8580 (m100) cc_final: 0.8139 (m100) REVERT: A 597 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7748 (pp20) REVERT: A 676 LEU cc_start: 0.8742 (mp) cc_final: 0.8165 (mp) REVERT: A 682 ASP cc_start: 0.8995 (t0) cc_final: 0.7844 (p0) REVERT: A 697 ASP cc_start: 0.9312 (t0) cc_final: 0.8285 (m-30) REVERT: A 707 PHE cc_start: 0.9204 (t80) cc_final: 0.8939 (t80) REVERT: B 22 PHE cc_start: 0.8212 (m-80) cc_final: 0.7860 (m-80) REVERT: B 40 MET cc_start: 0.9208 (ptm) cc_final: 0.8984 (ptm) REVERT: B 78 GLU cc_start: 0.9066 (mp0) cc_final: 0.8829 (mp0) REVERT: B 225 ASN cc_start: 0.8800 (t0) cc_final: 0.8485 (t0) REVERT: B 246 MET cc_start: 0.7713 (pmm) cc_final: 0.7303 (pmm) REVERT: B 267 GLU cc_start: 0.7840 (tt0) cc_final: 0.6626 (tm-30) REVERT: B 290 MET cc_start: 0.7111 (ttt) cc_final: 0.6419 (tpt) REVERT: B 331 GLU cc_start: 0.7115 (pm20) cc_final: 0.6396 (pp20) REVERT: B 343 MET cc_start: 0.8174 (mtp) cc_final: 0.7738 (mmm) REVERT: B 367 GLN cc_start: 0.8122 (mt0) cc_final: 0.7812 (mt0) REVERT: B 414 MET cc_start: 0.8958 (mmm) cc_final: 0.8036 (mmm) REVERT: B 452 ASN cc_start: 0.8145 (m-40) cc_final: 0.7465 (t0) REVERT: B 459 ILE cc_start: 0.9570 (mm) cc_final: 0.9304 (mm) REVERT: B 604 LEU cc_start: 0.8529 (tp) cc_final: 0.8251 (tp) REVERT: B 664 HIS cc_start: 0.6895 (m90) cc_final: 0.6643 (m-70) REVERT: B 673 SER cc_start: 0.8774 (t) cc_final: 0.8375 (p) REVERT: B 744 MET cc_start: 0.7670 (tpt) cc_final: 0.7309 (mmp) REVERT: C 11 MET cc_start: 0.8624 (mmt) cc_final: 0.7817 (mmm) REVERT: C 90 MET cc_start: 0.4261 (ttp) cc_final: 0.3865 (tpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2652 time to fit residues: 111.5409 Evaluate side-chains 237 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4357 r_free = 0.4357 target = 0.177103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134637 restraints weight = 122787.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139169 restraints weight = 64310.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.142624 restraints weight = 41830.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144483 restraints weight = 31778.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145259 restraints weight = 27066.282| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.7868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15257 Z= 0.105 Angle : 0.527 26.771 20678 Z= 0.273 Chirality : 0.037 0.148 2266 Planarity : 0.005 0.087 2583 Dihedral : 10.327 97.370 2307 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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 aren not related in a simple way. whole: -0.03 (0.20), residues: 1778 helix: 1.16 (0.18), residues: 809 sheet: -0.12 (0.38), residues: 197 loop : -1.27 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.011 0.001 TYR B 555 PHE 0.013 0.001 PHE A 191 TRP 0.012 0.001 TRP B 437 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00227 (15256) covalent geometry : angle 0.52688 (20676) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.64711 ( 2) hydrogen bonds : bond 0.03751 ( 729) hydrogen bonds : angle 4.50824 ( 2006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.843 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: A 232 TYR cc_start: 0.8585 (t80) cc_final: 0.7892 (t80) REVERT: A 282 PHE cc_start: 0.9053 (p90) cc_final: 0.8745 (p90) REVERT: A 437 HIS cc_start: 0.8469 (t70) cc_final: 0.8180 (m-70) REVERT: A 577 TRP cc_start: 0.8494 (m100) cc_final: 0.8161 (m100) REVERT: A 597 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7914 (pp20) REVERT: A 676 LEU cc_start: 0.8742 (mp) cc_final: 0.8160 (mp) REVERT: A 682 ASP cc_start: 0.8988 (t0) cc_final: 0.7805 (p0) REVERT: A 686 LEU cc_start: 0.9459 (tt) cc_final: 0.9158 (tp) REVERT: A 697 ASP cc_start: 0.9313 (t0) cc_final: 0.8266 (m-30) REVERT: A 707 PHE cc_start: 0.9197 (t80) cc_final: 0.8944 (t80) REVERT: B 22 PHE cc_start: 0.8220 (m-80) cc_final: 0.7785 (m-80) REVERT: B 44 ASN cc_start: 0.8608 (m-40) cc_final: 0.8334 (m110) REVERT: B 78 GLU cc_start: 0.9045 (mp0) cc_final: 0.8824 (mp0) REVERT: B 225 ASN cc_start: 0.8803 (t0) cc_final: 0.8481 (t0) REVERT: B 227 MET cc_start: 0.8629 (tpp) cc_final: 0.8428 (tpp) REVERT: B 246 MET cc_start: 0.7708 (pmm) cc_final: 0.7323 (pmm) REVERT: B 267 GLU cc_start: 0.7778 (tt0) cc_final: 0.6577 (tm-30) REVERT: B 290 MET cc_start: 0.7063 (ttt) cc_final: 0.6414 (tpt) REVERT: B 331 GLU cc_start: 0.7131 (pm20) cc_final: 0.6412 (pp20) REVERT: B 343 MET cc_start: 0.8295 (mtp) cc_final: 0.7966 (mmm) REVERT: B 367 GLN cc_start: 0.8423 (mt0) cc_final: 0.8101 (mt0) REVERT: B 414 MET cc_start: 0.8999 (mmm) cc_final: 0.8069 (mmm) REVERT: B 450 ILE cc_start: 0.9380 (mm) cc_final: 0.9055 (mm) REVERT: B 452 ASN cc_start: 0.8204 (m-40) cc_final: 0.7501 (t0) REVERT: B 459 ILE cc_start: 0.9574 (mm) cc_final: 0.9330 (mm) REVERT: B 507 MET cc_start: 0.4212 (mtm) cc_final: 0.3353 (tmm) REVERT: B 604 LEU cc_start: 0.8407 (tp) cc_final: 0.8138 (tp) REVERT: B 664 HIS cc_start: 0.6902 (m90) cc_final: 0.6659 (m-70) REVERT: B 673 SER cc_start: 0.8759 (t) cc_final: 0.8324 (p) REVERT: C 11 MET cc_start: 0.8644 (mmt) cc_final: 0.7891 (mmm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2543 time to fit residues: 106.1444 Evaluate side-chains 237 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 64 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4339 r_free = 0.4339 target = 0.175824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133181 restraints weight = 124252.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137694 restraints weight = 65429.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141224 restraints weight = 42619.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143013 restraints weight = 32242.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143803 restraints weight = 27436.191| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.8087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15257 Z= 0.112 Angle : 0.528 26.832 20678 Z= 0.274 Chirality : 0.037 0.209 2266 Planarity : 0.004 0.078 2583 Dihedral : 10.361 100.273 2307 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % 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 aren not related in a simple way. whole: 0.04 (0.20), residues: 1778 helix: 1.23 (0.18), residues: 808 sheet: -0.10 (0.38), residues: 197 loop : -1.24 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 124 TYR 0.017 0.001 TYR B 689 PHE 0.013 0.001 PHE B 496 TRP 0.012 0.001 TRP B 437 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00246 (15256) covalent geometry : angle 0.52821 (20676) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.58293 ( 2) hydrogen bonds : bond 0.03702 ( 729) hydrogen bonds : angle 4.49012 ( 2006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5275.43 seconds wall clock time: 90 minutes 41.17 seconds (5441.17 seconds total)