Starting phenix.real_space_refine on Sun Jul 5 15:34:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.map" model { file = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nka_12435/07_2026/7nka_12435.cif" } resolution = 4.07 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= 0.015 sd= 0.212 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 106 5.16 5 C 9303 2.51 5 N 2599 2.21 5 O 2879 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28778 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11704 Classifications: {'peptide': 735} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4075 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "F" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 729 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 3 Time building chain proxies: 5.00, per 1000 atoms: 0.17 Number of scatterers: 28778 At special positions: 0 Unit cell: (100.8, 113.4, 176.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 23 15.00 O 2879 8.00 N 2599 7.00 C 9303 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.01 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: 2.88 Conformation dependent library (CDL) restraints added in 869.4 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 17 sheets defined 49.6% alpha, 14.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.005A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.691A 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: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.634A 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: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.509A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.511A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.330A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.977A 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: 3.892A 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: 3.524A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.658A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.300A 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: 3.618A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A 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: 6.718A 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: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.690A 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: 6.065A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.612A 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: 6.718A 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: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.635A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.521A 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: 5.972A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.504A pdb=" N GLY F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 262 1.23 - 1.43: 6173 1.43 - 1.63: 8663 1.63 - 1.82: 183 Bond restraints: 29122 Sorted by residual: bond pdb=" CD ARG F 50 " pdb=" NE ARG F 50 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.40e-02 5.10e+03 6.59e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.40e-02 5.10e+03 6.53e+00 bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.42e+00 bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.36e+00 ... (remaining 29117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52262 5.65 - 11.30: 3 11.30 - 16.95: 0 16.95 - 22.60: 1 22.60 - 28.25: 5 Bond angle restraints: 52271 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.75 28.25 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 80.38 27.62 3.00e+00 1.11e-01 8.47e+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 81.88 27.12 3.00e+00 1.11e-01 8.17e+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 82.41 26.59 3.00e+00 1.11e-01 7.86e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.76 -26.86 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12545 17.93 - 35.86: 837 35.86 - 53.79: 241 53.79 - 71.72: 65 71.72 - 89.66: 11 Dihedral angle restraints: 13699 sinusoidal: 7646 harmonic: 6053 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1941 0.055 - 0.110: 268 0.110 - 0.165: 53 0.165 - 0.221: 12 0.221 - 0.276: 1 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA THR F 77 " pdb=" N THR F 77 " pdb=" C THR F 77 " pdb=" CB THR F 77 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN F 76 " pdb=" N ASN F 76 " pdb=" C ASN F 76 " pdb=" CB ASN F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP F 65 " pdb=" N ASP F 65 " pdb=" C ASP F 65 " pdb=" CB ASP F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 2272 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 67 " 0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE F 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE F 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 67 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.031 2.00e-02 2.50e+03 2.04e-02 8.35e+00 pdb=" CG TYR F 37 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 36 " -0.021 2.00e-02 2.50e+03 1.81e-02 8.15e+00 pdb=" CG TRP F 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP F 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 36 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 36 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP F 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 36 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 36 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 36 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP F 36 " -0.006 2.00e-02 2.50e+03 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1258 2.17 - 2.78: 56204 2.78 - 3.39: 80859 3.39 - 3.99: 105796 3.99 - 4.60: 165064 Nonbonded interactions: 409181 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 1.596 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409176 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: 0.560 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: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.950 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 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 0.048 15255 Z= 0.222 Angle : 0.672 26.857 20680 Z= 0.393 Chirality : 0.043 0.276 2275 Planarity : 0.005 0.085 2584 Dihedral : 13.485 89.655 5889 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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 are not related in a simple way. whole: -0.66 (0.19), residues: 1780 helix: 0.45 (0.19), residues: 786 sheet: -0.64 (0.37), residues: 184 loop : -1.23 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 66 TYR 0.033 0.002 TYR F 37 PHE 0.048 0.002 PHE A 446 TRP 0.030 0.002 TRP F 36 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.22 (15254) covalent geometry : angle 0.67122 / 0.39 (20678) SS BOND : bond 0.02132 / 1.02 ( 1) SS BOND : angle 2.84168 / 1.56 ( 2) hydrogen bonds : bond 0.14886 / 9.73 ( 733) hydrogen bonds : angle 5.96230 / 4.25 ( 2012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 502 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.818 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: A 257 ILE cc_start: 0.6131 (mt) cc_final: 0.5690 (mt) REVERT: A 272 ASP cc_start: 0.6141 (m-30) cc_final: 0.4867 (t0) REVERT: A 523 MET cc_start: 0.6118 (mtt) cc_final: 0.5332 (mtt) REVERT: A 602 VAL cc_start: 0.6611 (t) cc_final: 0.6282 (t) REVERT: B 132 THR cc_start: 0.6969 (m) cc_final: 0.6714 (m) REVERT: B 141 THR cc_start: 0.7205 (m) cc_final: 0.6992 (m) REVERT: B 218 LEU cc_start: 0.6427 (mt) cc_final: 0.6199 (tt) REVERT: B 277 GLU cc_start: 0.7326 (mp0) cc_final: 0.6792 (mm-30) REVERT: B 317 MET cc_start: 0.5153 (mmm) cc_final: 0.4524 (tpp) REVERT: B 417 THR cc_start: 0.7801 (m) cc_final: 0.7533 (m) REVERT: B 517 ILE cc_start: 0.7955 (mm) cc_final: 0.7626 (mm) REVERT: B 535 ILE cc_start: 0.6259 (mt) cc_final: 0.6003 (mt) REVERT: B 608 GLU cc_start: 0.6779 (tt0) cc_final: 0.6028 (pm20) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.3239 time to fit residues: 231.6340 Evaluate side-chains 322 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 437 HIS B 314 ASN B 425 ASN C 27 HIS F 5 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.205501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173088 restraints weight = 74363.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179326 restraints weight = 34630.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.183234 restraints weight = 19828.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185612 restraints weight = 13164.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.186676 restraints weight = 10028.558| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15255 Z= 0.160 Angle : 0.611 27.301 20680 Z= 0.322 Chirality : 0.039 0.155 2275 Planarity : 0.005 0.054 2584 Dihedral : 6.744 62.456 2230 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1780 helix: 0.39 (0.18), residues: 790 sheet: -0.45 (0.37), residues: 195 loop : -1.16 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 216 TYR 0.031 0.002 TYR C 115 PHE 0.022 0.002 PHE A 446 TRP 0.022 0.001 TRP A 368 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15254) covalent geometry : angle 0.61130 / 0.32 (20678) SS BOND : bond 0.00717 / 0.34 ( 1) SS BOND : angle 0.90759 / 0.48 ( 2) hydrogen bonds : bond 0.04910 / 3.20 ( 733) hydrogen bonds : angle 4.97801 / 3.53 ( 2012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 366 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.564 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: A 86 MET cc_start: 0.7392 (tpt) cc_final: 0.6897 (tpt) REVERT: A 155 MET cc_start: 0.5847 (tmm) cc_final: 0.4969 (tmm) REVERT: A 272 ASP cc_start: 0.7068 (m-30) cc_final: 0.5490 (t0) REVERT: A 523 MET cc_start: 0.5877 (mtt) cc_final: 0.5191 (mtt) REVERT: B 3 VAL cc_start: 0.7522 (t) cc_final: 0.7211 (t) REVERT: B 218 LEU cc_start: 0.7729 (mt) cc_final: 0.7345 (tp) REVERT: B 277 GLU cc_start: 0.7873 (mp0) cc_final: 0.7218 (mm-30) REVERT: B 608 GLU cc_start: 0.7271 (tt0) cc_final: 0.5981 (pm20) REVERT: B 609 VAL cc_start: 0.7444 (t) cc_final: 0.7094 (t) REVERT: B 655 MET cc_start: 0.8489 (ttm) cc_final: 0.8254 (ttm) REVERT: C 20 LEU cc_start: 0.8607 (mt) cc_final: 0.8387 (mm) REVERT: C 66 MET cc_start: 0.5152 (mmm) cc_final: 0.4906 (mtt) REVERT: C 196 CYS cc_start: 0.7200 (m) cc_final: 0.6623 (m) REVERT: C 206 MET cc_start: 0.7854 (tpp) cc_final: 0.7600 (tpp) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.2985 time to fit residues: 158.1616 Evaluate side-chains 274 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 ASN B 310 ASN B 425 ASN B 756 GLN C 27 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.199430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164186 restraints weight = 76149.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170302 restraints weight = 36477.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174194 restraints weight = 21357.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.176363 restraints weight = 14606.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177477 restraints weight = 11477.692| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15255 Z= 0.135 Angle : 0.567 25.755 20680 Z= 0.298 Chirality : 0.038 0.165 2275 Planarity : 0.004 0.047 2584 Dihedral : 6.661 68.427 2230 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1780 helix: 0.60 (0.19), residues: 792 sheet: -0.29 (0.36), residues: 202 loop : -1.12 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.014 0.001 TYR A 564 PHE 0.020 0.002 PHE A 446 TRP 0.008 0.001 TRP B 438 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15254) covalent geometry : angle 0.56688 / 0.30 (20678) SS BOND : bond 0.00387 / 0.18 ( 1) SS BOND : angle 0.76512 / 0.41 ( 2) hydrogen bonds : bond 0.04401 / 2.92 ( 733) hydrogen bonds : angle 4.65964 / 3.29 ( 2012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 344 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.821 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: A 86 MET cc_start: 0.7671 (tpt) cc_final: 0.7190 (tpp) REVERT: A 155 MET cc_start: 0.5665 (tmm) cc_final: 0.4827 (tmm) REVERT: A 272 ASP cc_start: 0.7417 (m-30) cc_final: 0.5953 (t0) REVERT: A 460 MET cc_start: 0.8051 (mtm) cc_final: 0.7737 (mmt) REVERT: A 523 MET cc_start: 0.6112 (mtt) cc_final: 0.5704 (mtt) REVERT: A 536 LYS cc_start: 0.6188 (ttpt) cc_final: 0.5910 (ptmt) REVERT: A 548 MET cc_start: 0.6520 (ttt) cc_final: 0.6285 (ttt) REVERT: A 597 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6693 (mt-10) REVERT: B 3 VAL cc_start: 0.7724 (t) cc_final: 0.7429 (t) REVERT: B 40 MET cc_start: 0.7629 (mtm) cc_final: 0.7311 (mtm) REVERT: B 52 LYS cc_start: 0.6925 (mtmt) cc_final: 0.6369 (tppt) REVERT: B 218 LEU cc_start: 0.7818 (mt) cc_final: 0.7582 (tp) REVERT: B 277 GLU cc_start: 0.7981 (mp0) cc_final: 0.7399 (mm-30) REVERT: B 321 MET cc_start: 0.6556 (mtm) cc_final: 0.6341 (ttm) REVERT: B 362 MET cc_start: 0.7494 (mmp) cc_final: 0.7179 (mmp) REVERT: B 418 VAL cc_start: 0.8315 (t) cc_final: 0.8070 (t) REVERT: B 480 LYS cc_start: 0.7079 (mmtm) cc_final: 0.6412 (mtmm) REVERT: B 608 GLU cc_start: 0.7029 (tt0) cc_final: 0.5906 (pm20) REVERT: B 609 VAL cc_start: 0.7572 (t) cc_final: 0.7252 (t) REVERT: C 20 LEU cc_start: 0.8725 (mt) cc_final: 0.8514 (mm) REVERT: C 64 MET cc_start: 0.7438 (ttm) cc_final: 0.7189 (ttm) REVERT: F 96 ASN cc_start: 0.7690 (t0) cc_final: 0.7389 (m-40) outliers start: 1 outliers final: 1 residues processed: 344 average time/residue: 0.2935 time to fit residues: 147.8644 Evaluate side-chains 270 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 ASN B 425 ASN B 537 ASN B 654 ASN B 664 HIS C 27 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153179 restraints weight = 75845.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158954 restraints weight = 37676.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162673 restraints weight = 22760.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165023 restraints weight = 15946.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166151 restraints weight = 12553.139| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15255 Z= 0.177 Angle : 0.618 28.082 20680 Z= 0.327 Chirality : 0.040 0.176 2275 Planarity : 0.005 0.061 2584 Dihedral : 6.866 72.889 2230 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1780 helix: 0.44 (0.18), residues: 800 sheet: -0.19 (0.36), residues: 198 loop : -1.26 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 174 TYR 0.021 0.002 TYR C 55 PHE 0.024 0.002 PHE A 520 TRP 0.028 0.002 TRP A 368 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (15254) covalent geometry : angle 0.61782 / 0.33 (20678) SS BOND : bond 0.00180 / 0.09 ( 1) SS BOND : angle 0.41233 / 0.22 ( 2) hydrogen bonds : bond 0.04718 / 3.13 ( 733) hydrogen bonds : angle 4.82757 / 3.39 ( 2012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 320 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.806 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: A 86 MET cc_start: 0.7696 (tpt) cc_final: 0.7167 (tpp) REVERT: A 155 MET cc_start: 0.5535 (tmm) cc_final: 0.4684 (tmm) REVERT: A 272 ASP cc_start: 0.7631 (m-30) cc_final: 0.6026 (t0) REVERT: A 597 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6870 (mm-30) REVERT: A 656 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6511 (mm-30) REVERT: B 218 LEU cc_start: 0.7675 (mt) cc_final: 0.7274 (tp) REVERT: B 277 GLU cc_start: 0.8049 (mp0) cc_final: 0.7425 (mm-30) REVERT: B 418 VAL cc_start: 0.8399 (t) cc_final: 0.8169 (t) REVERT: B 480 LYS cc_start: 0.7111 (mmtm) cc_final: 0.6360 (mtmm) REVERT: B 507 MET cc_start: 0.8929 (mtp) cc_final: 0.8717 (mtp) REVERT: B 608 GLU cc_start: 0.6955 (tt0) cc_final: 0.6184 (pm20) REVERT: B 609 VAL cc_start: 0.7990 (t) cc_final: 0.7477 (t) REVERT: B 616 MET cc_start: 0.5814 (mtp) cc_final: 0.5609 (mtp) REVERT: B 688 MET cc_start: 0.8549 (mmm) cc_final: 0.8324 (mtt) REVERT: C 64 MET cc_start: 0.7472 (ttm) cc_final: 0.7270 (ttm) REVERT: C 66 MET cc_start: 0.5890 (mmm) cc_final: 0.5667 (mtt) REVERT: C 83 ASP cc_start: 0.8485 (t0) cc_final: 0.8175 (t0) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2916 time to fit residues: 136.7621 Evaluate side-chains 258 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 0.0770 chunk 165 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 306 ASN B 425 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147902 restraints weight = 75866.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.153475 restraints weight = 37821.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157113 restraints weight = 23068.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.159302 restraints weight = 16279.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.160554 restraints weight = 12941.899| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15255 Z= 0.170 Angle : 0.597 25.949 20680 Z= 0.316 Chirality : 0.039 0.170 2275 Planarity : 0.005 0.049 2584 Dihedral : 6.958 77.587 2230 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1780 helix: 0.45 (0.18), residues: 800 sheet: -0.18 (0.36), residues: 195 loop : -1.33 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 116 TYR 0.017 0.002 TYR B 689 PHE 0.021 0.002 PHE A 520 TRP 0.013 0.002 TRP A 368 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (15254) covalent geometry : angle 0.59666 / 0.32 (20678) SS BOND : bond 0.00232 / 0.11 ( 1) SS BOND : angle 0.49512 / 0.29 ( 2) hydrogen bonds : bond 0.04649 / 3.12 ( 733) hydrogen bonds : angle 4.68773 / 3.29 ( 2012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 302 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.775 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: A 12 MET cc_start: 0.6270 (ppp) cc_final: 0.5957 (ppp) REVERT: A 86 MET cc_start: 0.7725 (tpt) cc_final: 0.7159 (tpp) REVERT: A 155 MET cc_start: 0.5439 (tmm) cc_final: 0.4560 (tmm) REVERT: A 272 ASP cc_start: 0.7643 (m-30) cc_final: 0.6915 (t0) REVERT: A 545 ILE cc_start: 0.8099 (pt) cc_final: 0.7881 (tp) REVERT: A 597 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6761 (mm-30) REVERT: A 656 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6715 (mm-30) REVERT: B 40 MET cc_start: 0.7536 (mtm) cc_final: 0.7115 (mtm) REVERT: B 218 LEU cc_start: 0.7837 (mt) cc_final: 0.7529 (tp) REVERT: B 277 GLU cc_start: 0.7838 (mp0) cc_final: 0.7551 (mm-30) REVERT: B 418 VAL cc_start: 0.8538 (t) cc_final: 0.8299 (t) REVERT: B 480 LYS cc_start: 0.7124 (mmtm) cc_final: 0.6494 (mtmm) REVERT: B 608 GLU cc_start: 0.7086 (tt0) cc_final: 0.6620 (pm20) REVERT: B 620 TYR cc_start: 0.5628 (t80) cc_final: 0.5426 (t80) REVERT: B 688 MET cc_start: 0.8630 (mmm) cc_final: 0.8328 (mtt) REVERT: C 20 LEU cc_start: 0.8415 (mm) cc_final: 0.7958 (mm) REVERT: C 64 MET cc_start: 0.7515 (ttm) cc_final: 0.7309 (ttm) REVERT: C 83 ASP cc_start: 0.8521 (t0) cc_final: 0.8046 (t0) REVERT: F 96 ASN cc_start: 0.8404 (t0) cc_final: 0.8130 (t0) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2697 time to fit residues: 120.2963 Evaluate side-chains 252 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 GLN B 306 ASN B 654 ASN C 73 GLN C 242 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.182890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145597 restraints weight = 75407.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151146 restraints weight = 37368.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154805 restraints weight = 22776.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.156934 restraints weight = 16036.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158413 restraints weight = 12779.669| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15255 Z= 0.142 Angle : 0.581 27.410 20680 Z= 0.305 Chirality : 0.039 0.168 2275 Planarity : 0.004 0.042 2584 Dihedral : 6.972 82.903 2230 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1780 helix: 0.67 (0.18), residues: 802 sheet: 0.02 (0.38), residues: 183 loop : -1.29 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 238 TYR 0.016 0.001 TYR A 334 PHE 0.020 0.002 PHE B 344 TRP 0.016 0.002 TRP A 368 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15254) covalent geometry : angle 0.58116 / 0.30 (20678) SS BOND : bond 0.00139 / 0.07 ( 1) SS BOND : angle 0.47272 / 0.28 ( 2) hydrogen bonds : bond 0.04434 / 2.97 ( 733) hydrogen bonds : angle 4.59913 / 3.23 ( 2012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 295 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 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: A 86 MET cc_start: 0.7575 (tpt) cc_final: 0.7294 (tpp) REVERT: A 155 MET cc_start: 0.5502 (tmm) cc_final: 0.4591 (tmm) REVERT: A 272 ASP cc_start: 0.7645 (m-30) cc_final: 0.7002 (t0) REVERT: A 537 TRP cc_start: 0.8112 (m100) cc_final: 0.7845 (m100) REVERT: A 545 ILE cc_start: 0.8223 (pt) cc_final: 0.7929 (tp) REVERT: A 597 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6754 (mm-30) REVERT: A 656 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6494 (mm-30) REVERT: B 218 LEU cc_start: 0.7826 (mt) cc_final: 0.7451 (tp) REVERT: B 277 GLU cc_start: 0.7856 (mp0) cc_final: 0.7533 (mm-30) REVERT: B 480 LYS cc_start: 0.7141 (mmtm) cc_final: 0.6592 (mtmm) REVERT: B 688 MET cc_start: 0.8545 (mmm) cc_final: 0.8327 (mtt) REVERT: B 718 MET cc_start: 0.8151 (mtp) cc_final: 0.7917 (mtp) REVERT: C 20 LEU cc_start: 0.8531 (mm) cc_final: 0.8111 (mm) REVERT: C 64 MET cc_start: 0.7410 (ttm) cc_final: 0.7179 (ttm) REVERT: C 83 ASP cc_start: 0.8461 (t0) cc_final: 0.8095 (t0) REVERT: F 18 LEU cc_start: 0.9037 (tt) cc_final: 0.8270 (tp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2760 time to fit residues: 120.1219 Evaluate side-chains 238 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 151 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.181945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145495 restraints weight = 74893.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150926 restraints weight = 36996.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154474 restraints weight = 22472.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.156495 restraints weight = 15783.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157487 restraints weight = 12609.892| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15255 Z= 0.128 Angle : 0.555 25.422 20680 Z= 0.288 Chirality : 0.038 0.159 2275 Planarity : 0.004 0.038 2584 Dihedral : 6.803 85.713 2230 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1780 helix: 0.87 (0.18), residues: 796 sheet: 0.17 (0.40), residues: 180 loop : -1.23 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 45 TYR 0.011 0.001 TYR C 111 PHE 0.016 0.001 PHE B 730 TRP 0.013 0.001 TRP A 368 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15254) covalent geometry : angle 0.55496 / 0.29 (20678) SS BOND : bond 0.00128 / 0.06 ( 1) SS BOND : angle 0.32795 / 0.19 ( 2) hydrogen bonds : bond 0.04179 / 2.79 ( 733) hydrogen bonds : angle 4.41505 / 3.10 ( 2012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.815 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: A 86 MET cc_start: 0.7599 (tpt) cc_final: 0.7284 (tpp) REVERT: A 155 MET cc_start: 0.5451 (tmm) cc_final: 0.4569 (tmm) REVERT: A 272 ASP cc_start: 0.7533 (m-30) cc_final: 0.7015 (t0) REVERT: A 537 TRP cc_start: 0.8087 (m100) cc_final: 0.7844 (m100) REVERT: A 581 MET cc_start: 0.8291 (ttm) cc_final: 0.7726 (ttm) REVERT: A 597 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6681 (mm-30) REVERT: B 3 VAL cc_start: 0.8255 (t) cc_final: 0.7998 (t) REVERT: B 40 MET cc_start: 0.7521 (mtm) cc_final: 0.7289 (mtm) REVERT: B 88 VAL cc_start: 0.7039 (t) cc_final: 0.6769 (t) REVERT: B 96 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5496 (tp30) REVERT: B 218 LEU cc_start: 0.7768 (mt) cc_final: 0.7491 (tp) REVERT: B 277 GLU cc_start: 0.7736 (mp0) cc_final: 0.7300 (mm-30) REVERT: B 347 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8375 (ptpp) REVERT: B 480 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6707 (mtmm) REVERT: B 718 MET cc_start: 0.8194 (mtp) cc_final: 0.7945 (mtp) REVERT: C 20 LEU cc_start: 0.8366 (mm) cc_final: 0.7887 (mm) REVERT: C 64 MET cc_start: 0.7262 (ttm) cc_final: 0.7010 (ttm) REVERT: C 83 ASP cc_start: 0.8428 (t0) cc_final: 0.8113 (t0) REVERT: C 206 MET cc_start: 0.8065 (tpp) cc_final: 0.7648 (tpp) REVERT: F 96 ASN cc_start: 0.8183 (t0) cc_final: 0.7982 (t0) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2760 time to fit residues: 116.6669 Evaluate side-chains 238 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 654 ASN C 73 GLN ** F 39 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 = 0.4228 r_free = 0.4228 target = 0.174290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137480 restraints weight = 76158.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142707 restraints weight = 38000.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145984 restraints weight = 23246.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148137 restraints weight = 16567.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149343 restraints weight = 13182.444| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15255 Z= 0.207 Angle : 0.668 28.294 20680 Z= 0.353 Chirality : 0.041 0.173 2275 Planarity : 0.005 0.083 2584 Dihedral : 7.086 90.575 2230 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1780 helix: 0.51 (0.18), residues: 796 sheet: -0.23 (0.38), residues: 192 loop : -1.48 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 350 TYR 0.020 0.002 TYR A 334 PHE 0.030 0.002 PHE A 520 TRP 0.021 0.002 TRP B 438 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (15254) covalent geometry : angle 0.66843 / 0.35 (20678) SS BOND : bond 0.00255 / 0.12 ( 1) SS BOND : angle 0.67151 / 0.39 ( 2) hydrogen bonds : bond 0.05142 / 3.44 ( 733) hydrogen bonds : angle 4.86816 / 3.42 ( 2012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 281 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.954 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: A 155 MET cc_start: 0.5584 (tmm) cc_final: 0.4612 (tmm) REVERT: A 272 ASP cc_start: 0.7796 (m-30) cc_final: 0.7211 (t0) REVERT: A 597 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6959 (mm-30) REVERT: B 1 MET cc_start: 0.7248 (mpp) cc_final: 0.6939 (mpp) REVERT: B 3 VAL cc_start: 0.8570 (t) cc_final: 0.8355 (t) REVERT: B 40 MET cc_start: 0.7941 (mtm) cc_final: 0.7576 (mtm) REVERT: B 218 LEU cc_start: 0.7900 (mt) cc_final: 0.7577 (tp) REVERT: B 256 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 277 GLU cc_start: 0.7855 (mp0) cc_final: 0.7371 (mm-30) REVERT: B 480 LYS cc_start: 0.7063 (mmtm) cc_final: 0.6775 (mtmm) REVERT: B 718 MET cc_start: 0.8325 (mtp) cc_final: 0.7985 (mtp) REVERT: C 20 LEU cc_start: 0.8168 (mm) cc_final: 0.7632 (mm) REVERT: C 64 MET cc_start: 0.7347 (ttm) cc_final: 0.7052 (ttm) REVERT: C 83 ASP cc_start: 0.8491 (t0) cc_final: 0.8235 (t0) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2720 time to fit residues: 112.5438 Evaluate side-chains 223 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 117 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN C 73 GLN ** F 39 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 = 0.4249 r_free = 0.4249 target = 0.176005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138930 restraints weight = 76055.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144150 restraints weight = 37680.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147623 restraints weight = 23150.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149792 restraints weight = 16387.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150883 restraints weight = 13019.385| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15255 Z= 0.134 Angle : 0.587 26.626 20680 Z= 0.305 Chirality : 0.038 0.165 2275 Planarity : 0.004 0.047 2584 Dihedral : 6.925 91.827 2230 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1780 helix: 0.78 (0.18), residues: 797 sheet: -0.24 (0.39), residues: 190 loop : -1.42 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 468 TYR 0.016 0.001 TYR A 334 PHE 0.017 0.002 PHE A 520 TRP 0.026 0.002 TRP F 110 HIS 0.005 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15254) covalent geometry : angle 0.58741 / 0.31 (20678) SS BOND : bond 0.00189 / 0.09 ( 1) SS BOND : angle 0.64953 / 0.37 ( 2) hydrogen bonds : bond 0.04526 / 3.04 ( 733) hydrogen bonds : angle 4.55417 / 3.19 ( 2012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 267 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.786 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: A 155 MET cc_start: 0.5563 (tmm) cc_final: 0.4578 (tmm) REVERT: A 272 ASP cc_start: 0.7648 (m-30) cc_final: 0.7183 (t0) REVERT: A 318 LYS cc_start: 0.7590 (tppt) cc_final: 0.7033 (tttt) REVERT: A 597 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6867 (mm-30) REVERT: A 662 SER cc_start: 0.8094 (t) cc_final: 0.7893 (t) REVERT: B 1 MET cc_start: 0.7238 (mpp) cc_final: 0.6946 (mpp) REVERT: B 3 VAL cc_start: 0.8501 (t) cc_final: 0.8283 (t) REVERT: B 40 MET cc_start: 0.7728 (mtm) cc_final: 0.7514 (mtm) REVERT: B 96 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5476 (tp30) REVERT: B 218 LEU cc_start: 0.7892 (mt) cc_final: 0.7610 (tp) REVERT: B 277 GLU cc_start: 0.7804 (mp0) cc_final: 0.7348 (mm-30) REVERT: B 347 LYS cc_start: 0.8773 (ptpp) cc_final: 0.8389 (ptpp) REVERT: B 480 LYS cc_start: 0.7042 (mmtm) cc_final: 0.6772 (mtmm) REVERT: B 718 MET cc_start: 0.8220 (mtp) cc_final: 0.7915 (mtp) REVERT: C 20 LEU cc_start: 0.8089 (mm) cc_final: 0.7564 (mm) REVERT: C 64 MET cc_start: 0.7317 (ttm) cc_final: 0.7049 (ttm) REVERT: C 82 ASN cc_start: 0.6989 (m-40) cc_final: 0.6367 (m-40) REVERT: C 87 ASP cc_start: 0.6883 (p0) cc_final: 0.6437 (p0) REVERT: F 96 ASN cc_start: 0.7857 (t0) cc_final: 0.7543 (m110) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2700 time to fit residues: 107.9716 Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN C 73 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** F 39 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 = 0.4255 r_free = 0.4255 target = 0.176557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139565 restraints weight = 75733.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144797 restraints weight = 37877.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.148219 restraints weight = 23287.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150007 restraints weight = 16568.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151614 restraints weight = 13462.238| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15255 Z= 0.117 Angle : 0.577 26.881 20680 Z= 0.298 Chirality : 0.038 0.170 2275 Planarity : 0.004 0.074 2584 Dihedral : 6.804 93.206 2230 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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 are not related in a simple way. whole: -0.22 (0.20), residues: 1780 helix: 0.98 (0.19), residues: 797 sheet: -0.09 (0.39), residues: 190 loop : -1.33 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 45 TYR 0.012 0.001 TYR A 334 PHE 0.024 0.001 PHE B 512 TRP 0.016 0.001 TRP A 368 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15254) covalent geometry : angle 0.57677 / 0.30 (20678) SS BOND : bond 0.00175 / 0.08 ( 1) SS BOND : angle 0.61792 / 0.35 ( 2) hydrogen bonds : bond 0.04244 / 2.85 ( 733) hydrogen bonds : angle 4.43909 / 3.10 ( 2012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5551 (tmm) cc_final: 0.4571 (tmm) REVERT: A 204 ARG cc_start: 0.6659 (tmm-80) cc_final: 0.6423 (ttp80) REVERT: A 272 ASP cc_start: 0.7584 (m-30) cc_final: 0.7250 (t0) REVERT: A 318 LYS cc_start: 0.7575 (tppt) cc_final: 0.7073 (tttt) REVERT: A 597 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6839 (mm-30) REVERT: A 662 SER cc_start: 0.8121 (t) cc_final: 0.7910 (t) REVERT: B 1 MET cc_start: 0.7204 (mpp) cc_final: 0.6933 (mpp) REVERT: B 3 VAL cc_start: 0.8509 (t) cc_final: 0.8303 (t) REVERT: B 40 MET cc_start: 0.7744 (mtm) cc_final: 0.7518 (mtm) REVERT: B 218 LEU cc_start: 0.7822 (mt) cc_final: 0.7585 (tp) REVERT: B 277 GLU cc_start: 0.7772 (mp0) cc_final: 0.7356 (mm-30) REVERT: B 347 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8311 (ptpp) REVERT: B 409 MET cc_start: 0.4407 (tmm) cc_final: 0.4177 (tmm) REVERT: B 480 LYS cc_start: 0.6887 (mmtm) cc_final: 0.6463 (mtmm) REVERT: B 718 MET cc_start: 0.8170 (mtp) cc_final: 0.7909 (mtp) REVERT: C 20 LEU cc_start: 0.8194 (mm) cc_final: 0.7731 (mm) REVERT: C 47 MET cc_start: 0.8583 (tpp) cc_final: 0.8356 (tpp) REVERT: C 64 MET cc_start: 0.7184 (ttm) cc_final: 0.6876 (ttm) REVERT: C 82 ASN cc_start: 0.6940 (m-40) cc_final: 0.6318 (m-40) REVERT: C 87 ASP cc_start: 0.6955 (p0) cc_final: 0.6519 (p0) REVERT: C 243 MET cc_start: 0.4825 (ppp) cc_final: 0.4556 (ppp) REVERT: F 96 ASN cc_start: 0.7813 (t0) cc_final: 0.7475 (m110) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2436 time to fit residues: 99.1276 Evaluate side-chains 223 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140281 restraints weight = 76368.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145604 restraints weight = 38109.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149154 restraints weight = 23398.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151337 restraints weight = 16528.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152458 restraints weight = 13123.488| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 15255 Z= 0.115 Angle : 0.564 26.658 20680 Z= 0.289 Chirality : 0.038 0.156 2275 Planarity : 0.004 0.046 2584 Dihedral : 6.719 94.529 2230 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1780 helix: 1.10 (0.19), residues: 797 sheet: -0.11 (0.39), residues: 192 loop : -1.32 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.013 0.001 TYR B 82 PHE 0.014 0.001 PHE B 730 TRP 0.016 0.001 TRP A 368 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15254) covalent geometry : angle 0.56421 / 0.29 (20678) SS BOND : bond 0.00178 / 0.08 ( 1) SS BOND : angle 0.59662 / 0.34 ( 2) hydrogen bonds : bond 0.04056 / 2.70 ( 733) hydrogen bonds : angle 4.32367 / 3.02 ( 2012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.60 seconds wall clock time: 88 minutes 16.10 seconds (5296.10 seconds total)