Starting phenix.real_space_refine on Sun Jul 5 15:01:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkc_12437/07_2026/7nkc_12437.map" } resolution = 4.46 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= 0.020 sd= 0.211 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 9319 2.51 5 N 2598 2.21 5 O 2874 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28788 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: "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: "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: "F" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 3 Time building chain proxies: 5.08, per 1000 atoms: 0.18 Number of scatterers: 28788 At special positions: 0 Unit cell: (98, 130.2, 124.6, 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 2874 8.00 N 2598 7.00 C 9319 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 856.9 milliseconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 18 sheets defined 50.0% alpha, 14.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.141A 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: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.432A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.636A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.636A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.731A 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: 3.530A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.827A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.588A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.617A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.331A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.979A 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: 3.894A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.108A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.523A 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: 3.660A 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 61 through 65 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.816A 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: 6.716A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.860A 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: 5.688A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A 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: 6.175A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.633A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.359A pdb=" N GLY F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.359A pdb=" N GLY F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) 731 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: 7.02 Time building geometry restraints manager: 3.98 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: 120 1.23 - 1.43: 6333 1.43 - 1.62: 8661 1.62 - 1.82: 183 Bond restraints: 29138 Sorted by residual: bond pdb=" C LYS F 76 " pdb=" O LYS F 76 " ideal model delta sigma weight residual 1.235 1.180 0.054 1.41e-02 5.03e+03 1.48e+01 bond pdb=" C LYS F 76 " pdb=" N ASN F 77 " ideal model delta sigma weight residual 1.333 1.385 -0.052 1.39e-02 5.18e+03 1.39e+01 bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.515 1.482 0.033 9.30e-03 1.16e+04 1.26e+01 bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.40e-02 5.10e+03 8.75e+00 bond pdb=" N ASP F 73 " pdb=" CA ASP F 73 " ideal model delta sigma weight residual 1.461 1.426 0.035 1.19e-02 7.06e+03 8.45e+00 ... (remaining 29133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52269 5.65 - 11.29: 16 11.29 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.23: 5 Bond angle restraints: 52291 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.77 28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.37 27.63 3.00e+00 1.11e-01 8.48e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.82 27.18 3.00e+00 1.11e-01 8.21e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.42 26.58 3.00e+00 1.11e-01 7.85e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.74 -26.84 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12516 17.93 - 35.87: 855 35.87 - 53.80: 249 53.80 - 71.73: 68 71.73 - 89.67: 10 Dihedral angle restraints: 13698 sinusoidal: 7647 harmonic: 6051 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 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+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 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 13695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2031 0.066 - 0.132: 203 0.132 - 0.197: 28 0.197 - 0.263: 5 0.263 - 0.329: 1 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA VAL F 2 " pdb=" N VAL F 2 " pdb=" C VAL F 2 " pdb=" CB VAL F 2 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA CYS F 22 " pdb=" N CYS F 22 " pdb=" C CYS F 22 " pdb=" CB CYS F 22 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE F 37 " pdb=" N PHE F 37 " pdb=" C PHE F 37 " pdb=" CB PHE F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2265 not shown) Planarity restraints: 4227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 117 " -0.167 2.00e-02 2.50e+03 1.16e-01 2.69e+02 pdb=" CG TYR F 117 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR F 117 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR F 117 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR F 117 " 0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR F 117 " 0.101 2.00e-02 2.50e+03 pdb=" CZ TYR F 117 " 0.069 2.00e-02 2.50e+03 pdb=" OH TYR F 117 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 118 " -0.186 2.00e-02 2.50e+03 8.69e-02 1.89e+02 pdb=" CG TRP F 118 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP F 118 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 TRP F 118 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP F 118 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 118 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP F 118 " 0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 118 " -0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 118 " 0.041 2.00e-02 2.50e+03 pdb=" CH2 TRP F 118 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 68 " -0.080 2.00e-02 2.50e+03 5.21e-02 4.75e+01 pdb=" CG PHE F 68 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE F 68 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE F 68 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 PHE F 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 68 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE F 68 " -0.063 2.00e-02 2.50e+03 ... (remaining 4224 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56237 2.78 - 3.39: 80894 3.39 - 3.99: 105787 3.99 - 4.60: 165154 Nonbonded interactions: 409334 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.604 2.450 nonbonded pdb="HG21 THR B 291 " pdb=" NZ LYS F 65 " model vdw 1.614 2.216 ... (remaining 409329 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: 0.340 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: 0.210 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2993 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 : 0.005 0.365 15272 Z= 0.380 Angle : 0.725 26.844 20700 Z= 0.430 Chirality : 0.043 0.329 2268 Planarity : 0.007 0.116 2586 Dihedral : 13.691 89.665 5892 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.25 % Allowed : 0.88 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1779 helix: 0.46 (0.19), residues: 786 sheet: -0.83 (0.36), residues: 185 loop : -1.36 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 38 TYR 0.222 0.004 TYR F 117 PHE 0.080 0.003 PHE F 68 TRP 0.186 0.004 TRP F 118 HIS 0.002 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.24 (15270) covalent geometry : angle 0.72417 / 0.43 (20698) SS BOND : bond 0.02088 / 0.99 ( 1) SS BOND : angle 3.32010 / 1.81 ( 2) hydrogen bonds : bond 0.15054 / 9.73 ( 732) hydrogen bonds : angle 5.94678 / 4.29 ( 2012) Misc. bond : bond 0.36523 / 17.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7214 (tp) cc_final: 0.6741 (tp) REVERT: A 284 LEU cc_start: 0.6053 (mt) cc_final: 0.5744 (mt) REVERT: B 1 MET cc_start: 0.2904 (tmm) cc_final: 0.2554 (tmm) REVERT: B 40 MET cc_start: 0.6958 (mtm) cc_final: 0.6026 (ttm) REVERT: B 227 MET cc_start: 0.6608 (ptm) cc_final: 0.5701 (mmp) REVERT: B 686 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8011 (tt0) REVERT: B 746 ILE cc_start: 0.6718 (mt) cc_final: 0.5836 (tt) REVERT: C 243 MET cc_start: 0.3584 (mtt) cc_final: 0.3250 (mmt) REVERT: F 36 TRP cc_start: -0.1932 (m100) cc_final: -0.2703 (m100) outliers start: 4 outliers final: 1 residues processed: 390 average time/residue: 0.3351 time to fit residues: 178.9168 Evaluate side-chains 257 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN B 105 ASN B 134 ASN B 145 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.233999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.197334 restraints weight = 88266.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.207395 restraints weight = 44553.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.213778 restraints weight = 24910.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.217971 restraints weight = 15209.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.220347 restraints weight = 10141.617| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4048 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15272 Z= 0.222 Angle : 0.674 27.623 20700 Z= 0.361 Chirality : 0.041 0.278 2268 Planarity : 0.005 0.055 2586 Dihedral : 6.903 66.421 2232 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -0.93 (0.19), residues: 1779 helix: 0.15 (0.18), residues: 807 sheet: -0.60 (0.36), residues: 199 loop : -1.39 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 72 TYR 0.026 0.002 TYR F 60 PHE 0.025 0.002 PHE A 611 TRP 0.023 0.002 TRP A 368 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (15270) covalent geometry : angle 0.67400 / 0.36 (20698) SS BOND : bond 0.00484 / 0.23 ( 1) SS BOND : angle 1.10450 / 0.63 ( 2) hydrogen bonds : bond 0.05424 / 3.63 ( 732) hydrogen bonds : angle 5.23520 / 3.73 ( 2012) Misc. bond : bond 0.00710 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8089 (t80) cc_final: 0.7452 (t80) REVERT: A 374 MET cc_start: 0.5265 (ttm) cc_final: 0.4995 (ttm) REVERT: A 576 LYS cc_start: 0.7766 (tmtt) cc_final: 0.7435 (tmtt) REVERT: A 579 MET cc_start: 0.6917 (ttp) cc_final: 0.6258 (ttp) REVERT: A 668 ILE cc_start: 0.5025 (mt) cc_final: 0.4684 (mt) REVERT: A 697 ASP cc_start: 0.7855 (t0) cc_final: 0.7585 (t0) REVERT: B 40 MET cc_start: 0.7008 (mtm) cc_final: 0.6212 (ttm) REVERT: B 165 ASP cc_start: 0.8399 (m-30) cc_final: 0.7854 (m-30) REVERT: B 227 MET cc_start: 0.8124 (ptm) cc_final: 0.5913 (mmp) REVERT: B 276 ASN cc_start: 0.7239 (m110) cc_final: 0.7003 (m110) REVERT: B 308 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8253 (mmmt) REVERT: B 392 ILE cc_start: 0.5162 (tp) cc_final: 0.4574 (tp) REVERT: B 414 MET cc_start: 0.6705 (tpt) cc_final: 0.5841 (tpt) REVERT: B 470 CYS cc_start: 0.7727 (m) cc_final: 0.7463 (m) REVERT: B 549 GLN cc_start: 0.7170 (mt0) cc_final: 0.6865 (mt0) REVERT: B 646 MET cc_start: 0.4725 (mtt) cc_final: 0.4274 (mtm) REVERT: C 27 HIS cc_start: 0.6980 (m170) cc_final: 0.6765 (m170) REVERT: C 48 LYS cc_start: 0.7886 (mttt) cc_final: 0.6697 (tptt) REVERT: C 90 MET cc_start: 0.4685 (mtm) cc_final: 0.4169 (mtm) REVERT: C 243 MET cc_start: 0.3049 (mtt) cc_final: 0.2471 (mmt) REVERT: F 36 TRP cc_start: 0.2462 (m100) cc_final: 0.1825 (m100) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3080 time to fit residues: 127.2887 Evaluate side-chains 248 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS B 306 ASN B 310 ASN B 346 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 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 = 0.4808 r_free = 0.4808 target = 0.223269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.186827 restraints weight = 89917.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.195957 restraints weight = 44906.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.201811 restraints weight = 25304.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.205445 restraints weight = 15816.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.208027 restraints weight = 11062.949| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4353 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 15272 Z= 0.198 Angle : 0.652 25.547 20700 Z= 0.351 Chirality : 0.040 0.177 2268 Planarity : 0.005 0.065 2586 Dihedral : 6.995 70.555 2232 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 1779 helix: 0.20 (0.18), residues: 789 sheet: -0.49 (0.37), residues: 195 loop : -1.55 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 151 TYR 0.021 0.002 TYR B 705 PHE 0.025 0.002 PHE B 254 TRP 0.020 0.002 TRP A 368 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (15270) covalent geometry : angle 0.65186 / 0.35 (20698) SS BOND : bond 0.00048 / 0.02 ( 1) SS BOND : angle 0.46130 / 0.27 ( 2) hydrogen bonds : bond 0.04931 / 3.29 ( 732) hydrogen bonds : angle 5.14099 / 3.64 ( 2012) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8116 (t80) cc_final: 0.7519 (t80) REVERT: A 374 MET cc_start: 0.5355 (ttm) cc_final: 0.5122 (ttm) REVERT: A 392 GLN cc_start: 0.6124 (mt0) cc_final: 0.5783 (mt0) REVERT: A 579 MET cc_start: 0.7693 (ttp) cc_final: 0.7446 (ttp) REVERT: A 581 MET cc_start: 0.8295 (mtp) cc_final: 0.8021 (ttm) REVERT: A 619 TRP cc_start: 0.6537 (m-90) cc_final: 0.6068 (m-90) REVERT: A 668 ILE cc_start: 0.5623 (mt) cc_final: 0.5352 (mt) REVERT: B 40 MET cc_start: 0.6731 (mtm) cc_final: 0.6264 (ttm) REVERT: B 163 LEU cc_start: 0.9257 (tp) cc_final: 0.9006 (tp) REVERT: B 165 ASP cc_start: 0.8643 (m-30) cc_final: 0.7714 (m-30) REVERT: B 227 MET cc_start: 0.8258 (ptm) cc_final: 0.5891 (mmp) REVERT: B 276 ASN cc_start: 0.7482 (m110) cc_final: 0.7256 (m110) REVERT: B 306 ASN cc_start: 0.6046 (m110) cc_final: 0.5629 (m-40) REVERT: B 308 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8344 (mmmt) REVERT: B 411 MET cc_start: 0.5791 (mpp) cc_final: 0.5483 (mpp) REVERT: B 450 ILE cc_start: 0.6465 (mp) cc_final: 0.6254 (mp) REVERT: B 490 PHE cc_start: 0.6953 (p90) cc_final: 0.6216 (p90) REVERT: B 497 TYR cc_start: 0.7002 (t80) cc_final: 0.6736 (t80) REVERT: C 48 LYS cc_start: 0.7859 (mttt) cc_final: 0.7084 (tptp) REVERT: C 53 MET cc_start: 0.4144 (mtm) cc_final: 0.3929 (ttp) REVERT: C 90 MET cc_start: 0.5045 (mtm) cc_final: 0.4373 (mtm) REVERT: C 202 MET cc_start: 0.8473 (tpt) cc_final: 0.8202 (tpt) REVERT: C 243 MET cc_start: 0.3275 (mtt) cc_final: 0.2616 (mmt) REVERT: F 36 TRP cc_start: 0.3090 (m100) cc_final: 0.2392 (m100) outliers start: 2 outliers final: 1 residues processed: 281 average time/residue: 0.3025 time to fit residues: 120.8757 Evaluate side-chains 246 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 17 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 670 GLN B 32 HIS B 137 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.212645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.174592 restraints weight = 94024.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183511 restraints weight = 47595.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.189353 restraints weight = 27358.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.193070 restraints weight = 17499.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.195501 restraints weight = 12424.233| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15272 Z= 0.260 Angle : 0.775 29.148 20700 Z= 0.414 Chirality : 0.043 0.265 2268 Planarity : 0.007 0.123 2586 Dihedral : 7.729 78.099 2232 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 1779 helix: -0.24 (0.17), residues: 793 sheet: -0.63 (0.37), residues: 190 loop : -1.90 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 230 TYR 0.044 0.003 TYR B 705 PHE 0.037 0.003 PHE A 205 TRP 0.027 0.002 TRP A 368 HIS 0.021 0.002 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (15270) covalent geometry : angle 0.77447 / 0.41 (20698) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 1.27452 / 0.70 ( 2) hydrogen bonds : bond 0.05508 / 3.73 ( 732) hydrogen bonds : angle 5.65590 / 4.02 ( 2012) Misc. bond : bond 0.00029 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8061 (t80) cc_final: 0.7484 (t80) REVERT: A 581 MET cc_start: 0.8530 (mtp) cc_final: 0.8283 (ttm) REVERT: A 647 ASN cc_start: 0.8863 (m-40) cc_final: 0.8549 (m110) REVERT: A 668 ILE cc_start: 0.6286 (mt) cc_final: 0.5988 (mt) REVERT: B 40 MET cc_start: 0.6866 (mtm) cc_final: 0.6101 (ttm) REVERT: B 89 LEU cc_start: 0.9501 (mt) cc_final: 0.9299 (mt) REVERT: B 163 LEU cc_start: 0.9411 (tp) cc_final: 0.9137 (tp) REVERT: B 165 ASP cc_start: 0.8565 (m-30) cc_final: 0.8165 (m-30) REVERT: B 227 MET cc_start: 0.8363 (ptm) cc_final: 0.6070 (mmp) REVERT: B 230 ASP cc_start: 0.7734 (t0) cc_final: 0.7529 (t70) REVERT: B 287 ARG cc_start: -0.0125 (ptt180) cc_final: -0.0396 (ptt180) REVERT: B 310 ASN cc_start: 0.8851 (m-40) cc_final: 0.8346 (m-40) REVERT: C 18 GLU cc_start: 0.7498 (tt0) cc_final: 0.7125 (tm-30) REVERT: C 55 TYR cc_start: 0.4782 (m-80) cc_final: 0.4288 (m-80) REVERT: C 90 MET cc_start: 0.5338 (mtm) cc_final: 0.4673 (mtm) REVERT: C 243 MET cc_start: 0.3456 (mtt) cc_final: 0.2707 (mmt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3167 time to fit residues: 128.6688 Evaluate side-chains 251 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 111 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 172 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN F 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.215513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.176495 restraints weight = 95432.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.185749 restraints weight = 47993.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.191833 restraints weight = 27529.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.195689 restraints weight = 17541.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.198276 restraints weight = 12373.323| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4675 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15272 Z= 0.136 Angle : 0.596 25.714 20700 Z= 0.317 Chirality : 0.039 0.162 2268 Planarity : 0.005 0.091 2586 Dihedral : 7.405 79.358 2232 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.13 % Allowed : 1.70 % 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: -0.97 (0.19), residues: 1779 helix: 0.34 (0.18), residues: 785 sheet: -0.53 (0.37), residues: 199 loop : -1.67 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 572 TYR 0.025 0.002 TYR B 705 PHE 0.019 0.002 PHE A 480 TRP 0.021 0.001 TRP A 368 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15270) covalent geometry : angle 0.59641 / 0.32 (20698) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.58164 / 0.32 ( 2) hydrogen bonds : bond 0.04619 / 3.17 ( 732) hydrogen bonds : angle 5.04394 / 3.56 ( 2012) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8240 (t80) cc_final: 0.7612 (t80) REVERT: A 638 ARG cc_start: 0.4654 (mtm-85) cc_final: 0.4262 (mtt-85) REVERT: A 645 VAL cc_start: 0.8602 (t) cc_final: 0.8307 (t) REVERT: A 647 ASN cc_start: 0.8536 (m-40) cc_final: 0.8185 (m110) REVERT: B 40 MET cc_start: 0.7002 (mtm) cc_final: 0.6407 (ttm) REVERT: B 163 LEU cc_start: 0.9306 (tp) cc_final: 0.9068 (tp) REVERT: B 165 ASP cc_start: 0.8449 (m-30) cc_final: 0.8087 (m-30) REVERT: B 227 MET cc_start: 0.8394 (ptm) cc_final: 0.6060 (mmp) REVERT: B 287 ARG cc_start: -0.0251 (ptt180) cc_final: -0.0710 (ttt180) REVERT: B 289 MET cc_start: 0.1965 (mmm) cc_final: 0.1684 (mmm) REVERT: B 290 MET cc_start: 0.5836 (tmm) cc_final: 0.5546 (tmm) REVERT: B 362 MET cc_start: 0.7457 (ptt) cc_final: 0.6809 (pmm) REVERT: B 411 MET cc_start: 0.5943 (mpp) cc_final: 0.5475 (mpp) REVERT: B 497 TYR cc_start: 0.7055 (t80) cc_final: 0.6833 (t80) REVERT: B 511 SER cc_start: 0.9150 (m) cc_final: 0.8914 (t) REVERT: B 517 ILE cc_start: 0.8107 (mt) cc_final: 0.7758 (mp) REVERT: B 669 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6907 (tptp) REVERT: C 53 MET cc_start: 0.4107 (mtm) cc_final: 0.3872 (ttp) REVERT: C 90 MET cc_start: 0.5209 (mtm) cc_final: 0.4387 (mtm) REVERT: C 202 MET cc_start: 0.8379 (tpt) cc_final: 0.7924 (tpt) REVERT: C 243 MET cc_start: 0.3278 (mtt) cc_final: 0.2502 (mmt) outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.2918 time to fit residues: 114.2081 Evaluate side-chains 246 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 110 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.212061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174234 restraints weight = 92139.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.183234 restraints weight = 45427.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.189060 restraints weight = 25772.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.192859 restraints weight = 16397.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.194948 restraints weight = 11543.524| |-----------------------------------------------------------------------------| r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4761 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15272 Z= 0.150 Angle : 0.595 26.376 20700 Z= 0.316 Chirality : 0.039 0.190 2268 Planarity : 0.004 0.073 2586 Dihedral : 7.515 83.393 2232 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % 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: -0.86 (0.19), residues: 1779 helix: 0.44 (0.18), residues: 789 sheet: -0.43 (0.38), residues: 194 loop : -1.64 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 46 TYR 0.024 0.002 TYR B 705 PHE 0.016 0.001 PHE B 730 TRP 0.026 0.002 TRP B 437 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15270) covalent geometry : angle 0.59523 / 0.32 (20698) SS BOND : bond 0.00094 / 0.04 ( 1) SS BOND : angle 0.84089 / 0.46 ( 2) hydrogen bonds : bond 0.04538 / 3.12 ( 732) hydrogen bonds : angle 5.05687 / 3.56 ( 2012) Misc. bond : bond 0.00067 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8182 (t80) cc_final: 0.7596 (t80) REVERT: A 442 ARG cc_start: 0.9503 (mtt180) cc_final: 0.9166 (ttm110) REVERT: A 638 ARG cc_start: 0.4952 (mtm-85) cc_final: 0.4581 (mtt-85) REVERT: A 647 ASN cc_start: 0.8855 (m-40) cc_final: 0.8514 (m110) REVERT: A 668 ILE cc_start: 0.6627 (mt) cc_final: 0.6383 (mt) REVERT: B 40 MET cc_start: 0.6791 (mtm) cc_final: 0.6121 (ttm) REVERT: B 163 LEU cc_start: 0.9394 (tp) cc_final: 0.9190 (tp) REVERT: B 165 ASP cc_start: 0.8397 (m-30) cc_final: 0.8011 (m-30) REVERT: B 287 ARG cc_start: -0.0393 (ptt180) cc_final: -0.0807 (ttt180) REVERT: B 289 MET cc_start: 0.2210 (mmm) cc_final: 0.1759 (mmm) REVERT: B 290 MET cc_start: 0.5922 (tmm) cc_final: 0.5635 (tmm) REVERT: B 362 MET cc_start: 0.7627 (ptt) cc_final: 0.6946 (pmm) REVERT: B 411 MET cc_start: 0.5991 (mpp) cc_final: 0.4817 (mpp) REVERT: B 497 TYR cc_start: 0.7089 (t80) cc_final: 0.6831 (t80) REVERT: B 509 LEU cc_start: 0.8297 (tp) cc_final: 0.7989 (tp) REVERT: B 511 SER cc_start: 0.9150 (m) cc_final: 0.8897 (t) REVERT: B 517 ILE cc_start: 0.8185 (mt) cc_final: 0.7881 (mp) REVERT: C 90 MET cc_start: 0.5299 (mtm) cc_final: 0.4631 (mtm) REVERT: C 243 MET cc_start: 0.3233 (mtt) cc_final: 0.2480 (mmt) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2838 time to fit residues: 111.3969 Evaluate side-chains 250 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 156 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN B 597 ASN B 629 ASN F 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.214627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177266 restraints weight = 92406.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.186295 restraints weight = 45551.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.192211 restraints weight = 25786.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.196187 restraints weight = 16292.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.198680 restraints weight = 11285.284| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4702 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15272 Z= 0.116 Angle : 0.563 27.079 20700 Z= 0.296 Chirality : 0.038 0.165 2268 Planarity : 0.004 0.061 2586 Dihedral : 7.405 86.616 2232 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.13 % Allowed : 0.44 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1779 helix: 0.71 (0.18), residues: 783 sheet: -0.32 (0.38), residues: 199 loop : -1.51 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 162 TYR 0.018 0.001 TYR B 705 PHE 0.016 0.001 PHE B 251 TRP 0.021 0.001 TRP A 368 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15270) covalent geometry : angle 0.56330 / 0.30 (20698) SS BOND : bond 0.00067 / 0.03 ( 1) SS BOND : angle 0.56638 / 0.31 ( 2) hydrogen bonds : bond 0.04229 / 2.90 ( 732) hydrogen bonds : angle 4.80972 / 3.39 ( 2012) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8170 (t80) cc_final: 0.7577 (t80) REVERT: A 445 TYR cc_start: 0.7918 (m-80) cc_final: 0.7716 (m-10) REVERT: A 607 MET cc_start: 0.4793 (mtt) cc_final: 0.4350 (mtt) REVERT: A 638 ARG cc_start: 0.4921 (mtm-85) cc_final: 0.4571 (mtt-85) REVERT: A 647 ASN cc_start: 0.8836 (m-40) cc_final: 0.8436 (m110) REVERT: A 668 ILE cc_start: 0.6673 (mt) cc_final: 0.6451 (mt) REVERT: B 40 MET cc_start: 0.6643 (mtm) cc_final: 0.5912 (ttm) REVERT: B 165 ASP cc_start: 0.8318 (m-30) cc_final: 0.7849 (m-30) REVERT: B 227 MET cc_start: 0.7259 (ptt) cc_final: 0.5723 (mmp) REVERT: B 287 ARG cc_start: -0.0490 (ptt180) cc_final: -0.0880 (ttt180) REVERT: B 289 MET cc_start: 0.1613 (mmm) cc_final: 0.1224 (mmm) REVERT: B 290 MET cc_start: 0.5867 (tmm) cc_final: 0.5621 (tmm) REVERT: B 362 MET cc_start: 0.7571 (ptt) cc_final: 0.6903 (pmm) REVERT: B 392 ILE cc_start: 0.5141 (tp) cc_final: 0.4668 (tp) REVERT: B 497 TYR cc_start: 0.7169 (t80) cc_final: 0.6942 (t80) REVERT: B 509 LEU cc_start: 0.8205 (tp) cc_final: 0.7911 (tp) REVERT: B 511 SER cc_start: 0.9186 (m) cc_final: 0.8926 (t) REVERT: B 517 ILE cc_start: 0.8152 (mt) cc_final: 0.7855 (mp) REVERT: B 669 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6763 (tttm) REVERT: C 53 MET cc_start: 0.4702 (mtm) cc_final: 0.4091 (ttp) REVERT: C 90 MET cc_start: 0.5531 (mtm) cc_final: 0.4476 (mtm) REVERT: C 202 MET cc_start: 0.8391 (tpt) cc_final: 0.7942 (tpt) REVERT: C 243 MET cc_start: 0.3220 (mtt) cc_final: 0.2452 (mmt) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.2823 time to fit residues: 111.1064 Evaluate side-chains 246 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 101 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 169 optimal weight: 0.0040 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN B 629 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.209486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.171092 restraints weight = 95622.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.179901 restraints weight = 47441.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.185689 restraints weight = 27168.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.189446 restraints weight = 17485.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.191639 restraints weight = 12486.389| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4886 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15272 Z= 0.145 Angle : 0.592 26.784 20700 Z= 0.314 Chirality : 0.039 0.315 2268 Planarity : 0.004 0.053 2586 Dihedral : 7.594 90.425 2232 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.13 % Allowed : 0.76 % 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: -0.68 (0.20), residues: 1779 helix: 0.56 (0.18), residues: 802 sheet: -0.35 (0.37), residues: 203 loop : -1.56 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 46 TYR 0.022 0.002 TYR B 705 PHE 0.015 0.001 PHE B 730 TRP 0.026 0.002 TRP A 368 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15270) covalent geometry : angle 0.59241 / 0.31 (20698) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.88836 / 0.48 ( 2) hydrogen bonds : bond 0.04399 / 3.03 ( 732) hydrogen bonds : angle 4.96949 / 3.51 ( 2012) Misc. bond : bond 0.00105 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0076 (ttt) cc_final: -0.0227 (ttt) REVERT: A 130 TYR cc_start: 0.8088 (t80) cc_final: 0.7499 (t80) REVERT: A 317 TRP cc_start: 0.7388 (p-90) cc_final: 0.7074 (p90) REVERT: A 548 MET cc_start: 0.4291 (mtp) cc_final: 0.4078 (mtp) REVERT: A 607 MET cc_start: 0.5085 (mtt) cc_final: 0.4696 (mtt) REVERT: A 619 TRP cc_start: 0.6844 (m-90) cc_final: 0.6629 (m-90) REVERT: A 638 ARG cc_start: 0.5008 (mtm-85) cc_final: 0.4690 (mtt-85) REVERT: A 668 ILE cc_start: 0.6829 (mt) cc_final: 0.6604 (mt) REVERT: B 40 MET cc_start: 0.6699 (mtm) cc_final: 0.5988 (ttm) REVERT: B 165 ASP cc_start: 0.8230 (m-30) cc_final: 0.7775 (m-30) REVERT: B 227 MET cc_start: 0.7523 (ptt) cc_final: 0.5818 (mmp) REVERT: B 289 MET cc_start: 0.1807 (mmm) cc_final: 0.1416 (mmm) REVERT: B 290 MET cc_start: 0.5683 (tmm) cc_final: 0.5420 (tmm) REVERT: B 310 ASN cc_start: 0.8802 (m-40) cc_final: 0.8572 (m-40) REVERT: B 348 MET cc_start: 0.6939 (mpp) cc_final: 0.6183 (mpp) REVERT: B 362 MET cc_start: 0.7617 (ptt) cc_final: 0.6943 (pmm) REVERT: B 392 ILE cc_start: 0.5026 (tp) cc_final: 0.4569 (tp) REVERT: B 511 SER cc_start: 0.9199 (m) cc_final: 0.8890 (t) REVERT: B 517 ILE cc_start: 0.8246 (mt) cc_final: 0.8026 (mp) REVERT: B 523 MET cc_start: 0.4801 (tpp) cc_final: 0.4459 (tpp) REVERT: B 669 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7211 (tptp) REVERT: C 53 MET cc_start: 0.4489 (mtm) cc_final: 0.4121 (ttm) REVERT: C 90 MET cc_start: 0.5686 (mtm) cc_final: 0.4639 (mtm) REVERT: C 164 MET cc_start: 0.6885 (mtm) cc_final: 0.6012 (mmm) REVERT: C 243 MET cc_start: 0.3279 (mtt) cc_final: 0.2457 (mmt) outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.3054 time to fit residues: 121.0327 Evaluate side-chains 252 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 90 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 122 optimal weight: 4.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 ASN F 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.208251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.169861 restraints weight = 94289.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178541 restraints weight = 46534.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.184218 restraints weight = 26665.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.187845 restraints weight = 17216.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.190425 restraints weight = 12415.257| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4908 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15272 Z= 0.145 Angle : 0.597 26.968 20700 Z= 0.316 Chirality : 0.039 0.215 2268 Planarity : 0.004 0.064 2586 Dihedral : 7.591 93.163 2232 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % 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: -0.68 (0.19), residues: 1779 helix: 0.55 (0.18), residues: 805 sheet: -0.37 (0.37), residues: 200 loop : -1.54 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.023 0.002 TYR B 705 PHE 0.015 0.001 PHE B 730 TRP 0.025 0.002 TRP A 368 HIS 0.004 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15270) covalent geometry : angle 0.59683 / 0.32 (20698) SS BOND : bond 0.00190 / 0.09 ( 1) SS BOND : angle 0.82353 / 0.44 ( 2) hydrogen bonds : bond 0.04392 / 3.03 ( 732) hydrogen bonds : angle 5.00115 / 3.50 ( 2012) Misc. bond : bond 0.00103 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0410 (ttt) cc_final: 0.0206 (ttt) REVERT: A 130 TYR cc_start: 0.8084 (t80) cc_final: 0.7479 (t80) REVERT: A 317 TRP cc_start: 0.7489 (p-90) cc_final: 0.7170 (p90) REVERT: A 445 TYR cc_start: 0.8474 (m-10) cc_final: 0.8243 (m-10) REVERT: A 607 MET cc_start: 0.4797 (mtt) cc_final: 0.4366 (mtt) REVERT: A 619 TRP cc_start: 0.7107 (m-90) cc_final: 0.6906 (m-90) REVERT: A 647 ASN cc_start: 0.8983 (m-40) cc_final: 0.8605 (m110) REVERT: A 668 ILE cc_start: 0.6933 (mt) cc_final: 0.6727 (mt) REVERT: B 40 MET cc_start: 0.6790 (mtm) cc_final: 0.5987 (ttm) REVERT: B 92 MET cc_start: 0.9009 (mmt) cc_final: 0.8721 (mmt) REVERT: B 163 LEU cc_start: 0.9231 (tp) cc_final: 0.8961 (tp) REVERT: B 165 ASP cc_start: 0.8252 (m-30) cc_final: 0.7833 (m-30) REVERT: B 227 MET cc_start: 0.7333 (ptt) cc_final: 0.5562 (mmp) REVERT: B 290 MET cc_start: 0.5674 (tmm) cc_final: 0.5424 (tmm) REVERT: B 362 MET cc_start: 0.7503 (ptt) cc_final: 0.6832 (pmm) REVERT: B 392 ILE cc_start: 0.4939 (tp) cc_final: 0.4339 (tp) REVERT: B 497 TYR cc_start: 0.7232 (t80) cc_final: 0.6892 (t80) REVERT: B 511 SER cc_start: 0.9199 (m) cc_final: 0.8867 (t) REVERT: B 664 HIS cc_start: 0.7627 (m-70) cc_final: 0.7007 (m-70) REVERT: B 669 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7305 (tptp) REVERT: B 714 MET cc_start: 0.1300 (ttt) cc_final: 0.1021 (ptm) REVERT: C 53 MET cc_start: 0.4413 (mtm) cc_final: 0.4047 (ttm) REVERT: C 90 MET cc_start: 0.5692 (mtm) cc_final: 0.4588 (mtm) REVERT: C 202 MET cc_start: 0.8325 (tpt) cc_final: 0.7783 (tpt) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.3093 time to fit residues: 125.0450 Evaluate side-chains 256 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 173 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 176 optimal weight: 0.0270 chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 545 GLN B 629 ASN C 160 GLN F 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.211075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.172864 restraints weight = 92181.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.181686 restraints weight = 45507.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.187644 restraints weight = 25811.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.191333 restraints weight = 16400.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.193312 restraints weight = 11656.680| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 moved from start: 0.8046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15272 Z= 0.110 Angle : 0.576 26.825 20700 Z= 0.300 Chirality : 0.038 0.193 2268 Planarity : 0.004 0.041 2586 Dihedral : 7.376 93.529 2232 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1779 helix: 0.78 (0.18), residues: 803 sheet: -0.27 (0.38), residues: 196 loop : -1.44 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.032 0.002 TYR B 431 PHE 0.030 0.001 PHE B 94 TRP 0.021 0.001 TRP A 368 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15270) covalent geometry : angle 0.57599 / 0.30 (20698) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.55375 / 0.32 ( 2) hydrogen bonds : bond 0.04250 / 2.92 ( 732) hydrogen bonds : angle 4.73261 / 3.31 ( 2012) Misc. bond : bond 0.00126 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8241 (t80) cc_final: 0.7674 (t80) REVERT: A 317 TRP cc_start: 0.7440 (p-90) cc_final: 0.7124 (p90) REVERT: A 445 TYR cc_start: 0.8381 (m-10) cc_final: 0.8155 (m-10) REVERT: A 537 TRP cc_start: 0.7877 (m100) cc_final: 0.7446 (m100) REVERT: A 548 MET cc_start: 0.4372 (mtp) cc_final: 0.4133 (mtp) REVERT: A 607 MET cc_start: 0.4877 (mtt) cc_final: 0.4457 (mtt) REVERT: A 619 TRP cc_start: 0.7019 (m-90) cc_final: 0.6775 (m-90) REVERT: A 638 ARG cc_start: 0.5031 (mtm-85) cc_final: 0.4772 (mtt-85) REVERT: A 647 ASN cc_start: 0.8931 (m-40) cc_final: 0.8568 (m110) REVERT: A 668 ILE cc_start: 0.6908 (mt) cc_final: 0.6704 (mt) REVERT: B 40 MET cc_start: 0.6682 (mtm) cc_final: 0.5909 (ttm) REVERT: B 92 MET cc_start: 0.8930 (mmt) cc_final: 0.8716 (mmt) REVERT: B 165 ASP cc_start: 0.8219 (m-30) cc_final: 0.7745 (m-30) REVERT: B 227 MET cc_start: 0.7110 (ptt) cc_final: 0.5696 (mmp) REVERT: B 287 ARG cc_start: -0.0345 (ptt180) cc_final: -0.0871 (ptt180) REVERT: B 362 MET cc_start: 0.7421 (ptt) cc_final: 0.6767 (pmm) REVERT: B 392 ILE cc_start: 0.4780 (tp) cc_final: 0.4145 (tp) REVERT: B 497 TYR cc_start: 0.7200 (t80) cc_final: 0.6844 (t80) REVERT: B 511 SER cc_start: 0.9177 (m) cc_final: 0.8861 (t) REVERT: B 517 ILE cc_start: 0.8226 (mt) cc_final: 0.8025 (mp) REVERT: B 523 MET cc_start: 0.4493 (tpp) cc_final: 0.4247 (tpp) REVERT: B 664 HIS cc_start: 0.7599 (m-70) cc_final: 0.6941 (m-70) REVERT: B 669 LYS cc_start: 0.7438 (ttpt) cc_final: 0.6980 (tttm) REVERT: B 714 MET cc_start: 0.0738 (ttt) cc_final: 0.0402 (ptm) REVERT: C 90 MET cc_start: 0.5618 (mtm) cc_final: 0.4532 (mtm) REVERT: C 202 MET cc_start: 0.8329 (tpt) cc_final: 0.7831 (tpt) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.3005 time to fit residues: 122.8197 Evaluate side-chains 257 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 165 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 ASN F 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.209431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.171643 restraints weight = 94096.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.180469 restraints weight = 46473.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.186349 restraints weight = 26427.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.190009 restraints weight = 16836.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.192129 restraints weight = 11990.352| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15272 Z= 0.118 Angle : 0.578 26.782 20700 Z= 0.303 Chirality : 0.038 0.197 2268 Planarity : 0.004 0.040 2586 Dihedral : 7.342 94.494 2232 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.06 % Allowed : 0.13 % 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: -0.38 (0.20), residues: 1779 helix: 0.87 (0.18), residues: 797 sheet: -0.26 (0.38), residues: 195 loop : -1.43 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.017 0.001 TYR B 705 PHE 0.029 0.001 PHE C 119 TRP 0.022 0.002 TRP A 368 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15270) covalent geometry : angle 0.57826 / 0.30 (20698) SS BOND : bond 0.00149 / 0.07 ( 1) SS BOND : angle 0.60072 / 0.32 ( 2) hydrogen bonds : bond 0.04120 / 2.83 ( 732) hydrogen bonds : angle 4.76752 / 3.33 ( 2012) Misc. bond : bond 0.00144 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4988.35 seconds wall clock time: 86 minutes 0.44 seconds (5160.44 seconds total)