Starting phenix.real_space_refine on Fri Mar 6 05:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkc_12437/03_2026/7nkc_12437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkc_12437/03_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_12437/03_2026/7nkc_12437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkc_12437/03_2026/7nkc_12437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nkc_12437/03_2026/7nkc_12437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkc_12437/03_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-5986/lib/python3.9/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: 4.92, per 1000 atoms: 0.17 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: 2.46 Conformation dependent library (CDL) restraints added in 899.4 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: 4.95 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: 6.85 Time building geometry restraints manager: 3.44 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: 12551 17.93 - 35.87: 865 35.87 - 53.80: 265 53.80 - 71.73: 88 71.73 - 89.67: 16 Dihedral angle restraints: 13785 sinusoidal: 7734 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 13782 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: 0.290 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3186 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 : 14.450 89.665 5970 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 covalent geometry : bond 0.00427 (15270) covalent geometry : angle 0.72417 (20698) SS BOND : bond 0.02088 ( 1) SS BOND : angle 3.32010 ( 2) hydrogen bonds : bond 0.15054 ( 732) hydrogen bonds : angle 5.94678 ( 2012) Misc. bond : bond 0.36523 ( 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 : 0.819 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: 0.3629 time to fit residues: 191.1019 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 : 0.856 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 134 ASN B 145 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.233126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.196697 restraints weight = 88266.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.206642 restraints weight = 44419.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.212825 restraints weight = 24806.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.217081 restraints weight = 15246.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.219469 restraints weight = 10145.664| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4302 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15272 Z= 0.248 Angle : 0.716 27.742 20700 Z= 0.383 Chirality : 0.042 0.267 2268 Planarity : 0.006 0.063 2586 Dihedral : 10.217 73.445 2310 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % 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: -1.05 (0.19), residues: 1779 helix: 0.04 (0.18), residues: 807 sheet: -0.62 (0.36), residues: 199 loop : -1.45 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 72 TYR 0.021 0.002 TYR B 705 PHE 0.024 0.002 PHE A 611 TRP 0.025 0.002 TRP A 368 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00473 (15270) covalent geometry : angle 0.71622 (20698) SS BOND : bond 0.00638 ( 1) SS BOND : angle 1.48834 ( 2) hydrogen bonds : bond 0.05330 ( 732) hydrogen bonds : angle 5.27484 ( 2012) Misc. bond : bond 0.00581 ( 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 300 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.759 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: A 130 TYR cc_start: 0.8065 (t80) cc_final: 0.7527 (t80) REVERT: A 374 MET cc_start: 0.5301 (ttm) cc_final: 0.5038 (ttm) REVERT: A 579 MET cc_start: 0.6990 (ttp) cc_final: 0.6333 (ttp) REVERT: A 668 ILE cc_start: 0.5100 (mt) cc_final: 0.4750 (mt) REVERT: A 697 ASP cc_start: 0.7972 (t0) cc_final: 0.7667 (t0) REVERT: B 40 MET cc_start: 0.7183 (mtm) cc_final: 0.6443 (ttm) REVERT: B 111 MET cc_start: 0.3613 (ttp) cc_final: 0.3407 (ttp) REVERT: B 165 ASP cc_start: 0.8516 (m-30) cc_final: 0.8016 (m-30) REVERT: B 227 MET cc_start: 0.8154 (ptm) cc_final: 0.5924 (mmp) REVERT: B 276 ASN cc_start: 0.7282 (m110) cc_final: 0.7043 (m110) REVERT: B 308 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8239 (mmmt) REVERT: B 392 ILE cc_start: 0.4780 (tp) cc_final: 0.4179 (tp) REVERT: B 414 MET cc_start: 0.7112 (tpt) cc_final: 0.6213 (tpt) REVERT: B 470 CYS cc_start: 0.7754 (m) cc_final: 0.7479 (m) REVERT: B 549 GLN cc_start: 0.7176 (mt0) cc_final: 0.6861 (mt0) REVERT: B 646 MET cc_start: 0.4730 (mtt) cc_final: 0.4311 (mtm) REVERT: C 27 HIS cc_start: 0.6812 (m170) cc_final: 0.6560 (m170) REVERT: C 48 LYS cc_start: 0.7859 (mttt) cc_final: 0.6869 (tptm) REVERT: C 90 MET cc_start: 0.4754 (mtm) cc_final: 0.4207 (mtm) REVERT: C 243 MET cc_start: 0.3093 (mtt) cc_final: 0.2500 (mmt) REVERT: F 36 TRP cc_start: 0.2966 (m100) cc_final: 0.2378 (m100) outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.3314 time to fit residues: 137.3183 Evaluate side-chains 253 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 7.9990 chunk 126 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 756 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.227890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.189876 restraints weight = 94103.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.199412 restraints weight = 47930.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.205550 restraints weight = 27340.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.209458 restraints weight = 17152.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.211867 restraints weight = 11869.933| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4413 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15272 Z= 0.157 Angle : 0.591 26.022 20700 Z= 0.315 Chirality : 0.039 0.170 2268 Planarity : 0.004 0.056 2586 Dihedral : 10.013 73.279 2310 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.13 % Allowed : 1.58 % Favored : 98.30 % 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: -0.84 (0.19), residues: 1779 helix: 0.35 (0.18), residues: 796 sheet: -0.59 (0.36), residues: 195 loop : -1.47 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 151 TYR 0.017 0.002 TYR C 55 PHE 0.017 0.002 PHE B 730 TRP 0.017 0.001 TRP A 368 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00327 (15270) covalent geometry : angle 0.59087 (20698) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.61195 ( 2) hydrogen bonds : bond 0.04642 ( 732) hydrogen bonds : angle 4.98384 ( 2012) Misc. bond : bond 0.00040 ( 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 275 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.840 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: A 130 TYR cc_start: 0.8163 (t80) cc_final: 0.7548 (t80) REVERT: A 392 GLN cc_start: 0.6039 (mt0) cc_final: 0.5585 (mt0) REVERT: A 548 MET cc_start: 0.5281 (mtt) cc_final: 0.4962 (mtt) REVERT: A 576 LYS cc_start: 0.7777 (tmtt) cc_final: 0.7468 (tmtt) REVERT: A 581 MET cc_start: 0.7983 (mtp) cc_final: 0.7780 (ttm) REVERT: A 668 ILE cc_start: 0.5218 (mt) cc_final: 0.4958 (mt) REVERT: B 40 MET cc_start: 0.6913 (mtm) cc_final: 0.6441 (ttm) REVERT: B 163 LEU cc_start: 0.9243 (tp) cc_final: 0.8738 (tp) REVERT: B 165 ASP cc_start: 0.8489 (m-30) cc_final: 0.7617 (m-30) REVERT: B 227 MET cc_start: 0.8195 (ptm) cc_final: 0.5829 (mmp) REVERT: B 276 ASN cc_start: 0.7374 (m110) cc_final: 0.7152 (m110) REVERT: B 306 ASN cc_start: 0.5807 (m110) cc_final: 0.5556 (m-40) REVERT: B 308 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8281 (mmmt) REVERT: B 414 MET cc_start: 0.7035 (tpt) cc_final: 0.6024 (tpt) REVERT: B 497 TYR cc_start: 0.6872 (t80) cc_final: 0.6608 (t80) REVERT: B 714 MET cc_start: 0.1467 (ttt) cc_final: 0.1118 (ttt) REVERT: C 90 MET cc_start: 0.4849 (mtm) cc_final: 0.4227 (mtm) REVERT: C 202 MET cc_start: 0.8395 (tpt) cc_final: 0.8105 (tpt) REVERT: C 243 MET cc_start: 0.3087 (mtt) cc_final: 0.2484 (mmt) REVERT: F 36 TRP cc_start: 0.3008 (m100) cc_final: 0.2631 (m100) outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3113 time to fit residues: 120.0615 Evaluate side-chains 245 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 20.0000 chunk 124 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 172 optimal weight: 0.0060 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 346 ASN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 664 HIS B 679 GLN ** 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 = 0.4782 r_free = 0.4782 target = 0.220726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.183896 restraints weight = 91474.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.193147 restraints weight = 45696.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.199070 restraints weight = 25787.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.202865 restraints weight = 16137.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.205043 restraints weight = 11228.919| |-----------------------------------------------------------------------------| r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4663 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15272 Z= 0.176 Angle : 0.627 27.895 20700 Z= 0.332 Chirality : 0.039 0.190 2268 Planarity : 0.005 0.080 2586 Dihedral : 10.103 74.042 2310 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % 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: -0.81 (0.19), residues: 1779 helix: 0.44 (0.18), residues: 780 sheet: -0.53 (0.36), residues: 205 loop : -1.52 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 116 TYR 0.023 0.002 TYR B 705 PHE 0.027 0.002 PHE B 94 TRP 0.020 0.002 TRP A 368 HIS 0.009 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00378 (15270) covalent geometry : angle 0.62744 (20698) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.71018 ( 2) hydrogen bonds : bond 0.04635 ( 732) hydrogen bonds : angle 5.03287 ( 2012) Misc. bond : bond 0.00007 ( 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 277 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.762 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: A 130 TYR cc_start: 0.8111 (t80) cc_final: 0.7558 (t80) REVERT: A 374 MET cc_start: 0.5365 (ttm) cc_final: 0.5037 (ttm) REVERT: A 470 LEU cc_start: 0.7969 (tp) cc_final: 0.7743 (tp) REVERT: A 619 TRP cc_start: 0.6590 (m-90) cc_final: 0.6189 (m-90) REVERT: A 661 GLU cc_start: 0.6268 (mt-10) cc_final: 0.6033 (mt-10) REVERT: A 690 ILE cc_start: 0.5726 (mt) cc_final: 0.5520 (mt) REVERT: A 697 ASP cc_start: 0.8288 (t0) cc_final: 0.8084 (t0) REVERT: B 40 MET cc_start: 0.6603 (mtm) cc_final: 0.6078 (ttm) REVERT: B 163 LEU cc_start: 0.9298 (tp) cc_final: 0.8807 (tp) REVERT: B 165 ASP cc_start: 0.8365 (m-30) cc_final: 0.7779 (m-30) REVERT: B 227 MET cc_start: 0.8329 (ptm) cc_final: 0.5877 (mmp) REVERT: B 287 ARG cc_start: 0.0191 (ptt180) cc_final: -0.0021 (ptt180) REVERT: B 306 ASN cc_start: 0.5733 (m110) cc_final: 0.5520 (m-40) REVERT: B 325 ILE cc_start: 0.7123 (mm) cc_final: 0.6869 (mm) REVERT: B 392 ILE cc_start: 0.4609 (tp) cc_final: 0.3951 (tp) REVERT: B 549 GLN cc_start: 0.7029 (mt0) cc_final: 0.6806 (mt0) REVERT: C 48 LYS cc_start: 0.7919 (mttt) cc_final: 0.7181 (tptp) REVERT: C 55 TYR cc_start: 0.4780 (m-80) cc_final: 0.4553 (m-80) REVERT: C 90 MET cc_start: 0.5246 (mtm) cc_final: 0.4561 (mtm) REVERT: C 202 MET cc_start: 0.8467 (tpt) cc_final: 0.8131 (tpt) REVERT: C 243 MET cc_start: 0.3308 (mtt) cc_final: 0.2646 (mmt) outliers start: 1 outliers final: 1 residues processed: 276 average time/residue: 0.2989 time to fit residues: 116.8505 Evaluate side-chains 254 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 172 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.218925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.180331 restraints weight = 94063.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.189845 restraints weight = 47401.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.195699 restraints weight = 26913.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.199499 restraints weight = 17159.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.202004 restraints weight = 12106.359| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15272 Z= 0.162 Angle : 0.600 26.278 20700 Z= 0.321 Chirality : 0.039 0.185 2268 Planarity : 0.005 0.075 2586 Dihedral : 10.152 77.422 2310 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -0.78 (0.19), residues: 1779 helix: 0.51 (0.18), residues: 782 sheet: -0.59 (0.36), residues: 204 loop : -1.52 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 572 TYR 0.025 0.002 TYR B 705 PHE 0.017 0.002 PHE B 333 TRP 0.020 0.001 TRP A 368 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00341 (15270) covalent geometry : angle 0.59983 (20698) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.71600 ( 2) hydrogen bonds : bond 0.04512 ( 732) hydrogen bonds : angle 5.00368 ( 2012) Misc. bond : bond 0.00029 ( 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 272 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8235 (t80) cc_final: 0.7647 (t80) REVERT: A 311 MET cc_start: -0.3157 (ptt) cc_final: -0.3475 (ptt) REVERT: A 619 TRP cc_start: 0.6804 (m-90) cc_final: 0.6470 (m-90) REVERT: A 638 ARG cc_start: 0.4741 (mtm-85) cc_final: 0.4233 (mtt-85) REVERT: A 645 VAL cc_start: 0.8356 (t) cc_final: 0.8094 (t) REVERT: A 668 ILE cc_start: 0.5938 (mt) cc_final: 0.5615 (mt) REVERT: A 670 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7360 (mm-40) REVERT: B 40 MET cc_start: 0.6636 (mtm) cc_final: 0.6092 (ttm) REVERT: B 163 LEU cc_start: 0.9301 (tp) cc_final: 0.9033 (tp) REVERT: B 165 ASP cc_start: 0.8286 (m-30) cc_final: 0.7886 (m-30) REVERT: B 287 ARG cc_start: -0.0222 (ptt180) cc_final: -0.0600 (ptt-90) REVERT: B 290 MET cc_start: 0.5883 (tmm) cc_final: 0.5569 (tmm) REVERT: B 306 ASN cc_start: 0.6219 (m110) cc_final: 0.5887 (m-40) REVERT: B 669 LYS cc_start: 0.7376 (ttpt) cc_final: 0.6717 (tttm) REVERT: C 48 LYS cc_start: 0.7890 (mttt) cc_final: 0.7175 (tptp) REVERT: C 90 MET cc_start: 0.5442 (mtm) cc_final: 0.4375 (mtm) REVERT: C 243 MET cc_start: 0.3284 (mtt) cc_final: 0.2635 (mmt) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3193 time to fit residues: 121.3727 Evaluate side-chains 242 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 10.0000 chunk 166 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 134 ASN B 276 ASN B 284 ASN B 310 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.202397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.163977 restraints weight = 101726.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.172613 restraints weight = 51683.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.178007 restraints weight = 30006.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.181105 restraints weight = 19590.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.183668 restraints weight = 14540.136| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5319 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15272 Z= 0.318 Angle : 0.846 27.897 20700 Z= 0.462 Chirality : 0.045 0.207 2268 Planarity : 0.008 0.187 2586 Dihedral : 11.097 93.060 2310 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 28.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.26 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.90 (0.18), residues: 1779 helix: -0.63 (0.17), residues: 786 sheet: -0.80 (0.38), residues: 187 loop : -1.99 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 230 TYR 0.065 0.004 TYR B 705 PHE 0.024 0.003 PHE B 94 TRP 0.070 0.004 TRP B 437 HIS 0.007 0.002 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00629 (15270) covalent geometry : angle 0.84582 (20698) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.77108 ( 2) hydrogen bonds : bond 0.06147 ( 732) hydrogen bonds : angle 6.01617 ( 2012) Misc. bond : bond 0.00202 ( 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: 0 poor density : 275 time to evaluate : 0.710 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: 0.8268 (t80) cc_final: 0.7620 (t80) REVERT: A 311 MET cc_start: -0.2286 (ptt) cc_final: -0.2954 (ptt) REVERT: A 374 MET cc_start: 0.5308 (ttm) cc_final: 0.4920 (ttt) REVERT: A 410 GLU cc_start: 0.8873 (tt0) cc_final: 0.8548 (tt0) REVERT: A 581 MET cc_start: 0.8909 (ttm) cc_final: 0.8343 (ttm) REVERT: A 668 ILE cc_start: 0.7086 (mt) cc_final: 0.6859 (mt) REVERT: A 670 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7360 (mm-40) REVERT: B 40 MET cc_start: 0.6968 (mtm) cc_final: 0.6191 (ttm) REVERT: B 165 ASP cc_start: 0.8658 (m-30) cc_final: 0.8347 (m-30) REVERT: B 227 MET cc_start: 0.6994 (ptt) cc_final: 0.5751 (tpt) REVERT: B 290 MET cc_start: 0.5951 (tmm) cc_final: 0.5655 (tmm) REVERT: B 450 ILE cc_start: 0.6800 (mt) cc_final: 0.6568 (mt) REVERT: B 511 SER cc_start: 0.9171 (m) cc_final: 0.8860 (t) REVERT: B 517 ILE cc_start: 0.8402 (mt) cc_final: 0.8128 (mp) REVERT: B 646 MET cc_start: 0.4396 (mtt) cc_final: 0.3886 (mtp) REVERT: B 664 HIS cc_start: 0.7680 (m-70) cc_final: 0.6936 (m-70) REVERT: C 90 MET cc_start: 0.5763 (mtm) cc_final: 0.4800 (mtm) REVERT: C 120 GLU cc_start: 0.8676 (mp0) cc_final: 0.8412 (mp0) REVERT: C 236 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6437 (mm-40) REVERT: C 243 MET cc_start: 0.3355 (mtt) cc_final: 0.2414 (mmt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3067 time to fit residues: 119.8267 Evaluate side-chains 247 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 582 GLN B 597 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.208949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.169792 restraints weight = 96439.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.178696 restraints weight = 48014.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.184403 restraints weight = 27606.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.187801 restraints weight = 17897.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.190375 restraints weight = 13224.997| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5105 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15272 Z= 0.136 Angle : 0.613 25.501 20700 Z= 0.327 Chirality : 0.039 0.187 2268 Planarity : 0.005 0.092 2586 Dihedral : 10.643 89.417 2310 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % 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: -1.15 (0.19), residues: 1779 helix: 0.19 (0.18), residues: 789 sheet: -0.49 (0.38), residues: 193 loop : -1.80 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 116 TYR 0.031 0.002 TYR B 705 PHE 0.037 0.002 PHE B 94 TRP 0.027 0.002 TRP B 437 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00297 (15270) covalent geometry : angle 0.61289 (20698) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.58498 ( 2) hydrogen bonds : bond 0.04706 ( 732) hydrogen bonds : angle 5.18817 ( 2012) Misc. bond : bond 0.00101 ( 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 272 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.794 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: 0.8182 (t80) cc_final: 0.7562 (t80) REVERT: A 311 MET cc_start: -0.2516 (ptt) cc_final: -0.3021 (ptt) REVERT: A 374 MET cc_start: 0.5149 (ttm) cc_final: 0.4883 (ttt) REVERT: A 392 GLN cc_start: 0.5771 (mt0) cc_final: 0.5015 (mt0) REVERT: A 581 MET cc_start: 0.8727 (ttm) cc_final: 0.8495 (ttm) REVERT: A 668 ILE cc_start: 0.6892 (mt) cc_final: 0.6639 (mt) REVERT: A 670 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7316 (mm-40) REVERT: B 40 MET cc_start: 0.6867 (mtm) cc_final: 0.6037 (ttm) REVERT: B 165 ASP cc_start: 0.8484 (m-30) cc_final: 0.7961 (m-30) REVERT: B 227 MET cc_start: 0.6584 (ptt) cc_final: 0.5611 (tpt) REVERT: B 411 MET cc_start: 0.6233 (mpp) cc_final: 0.5730 (mpp) REVERT: B 479 LYS cc_start: 0.5624 (ptpp) cc_final: 0.5043 (mttt) REVERT: B 511 SER cc_start: 0.9142 (m) cc_final: 0.8827 (t) REVERT: B 654 ASN cc_start: 0.6072 (p0) cc_final: 0.4806 (t0) REVERT: B 664 HIS cc_start: 0.7625 (m-70) cc_final: 0.6964 (m-70) REVERT: C 243 MET cc_start: 0.3233 (mtt) cc_final: 0.2421 (mmt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3048 time to fit residues: 118.8233 Evaluate side-chains 247 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 0.2980 chunk 154 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 228 ASN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 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 = 0.4656 r_free = 0.4656 target = 0.206580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.167897 restraints weight = 95891.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.176657 restraints weight = 47429.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.182362 restraints weight = 27217.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.186018 restraints weight = 17510.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.188056 restraints weight = 12532.809| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15272 Z= 0.157 Angle : 0.617 27.024 20700 Z= 0.330 Chirality : 0.040 0.343 2268 Planarity : 0.005 0.075 2586 Dihedral : 10.631 90.636 2310 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -1.05 (0.19), residues: 1779 helix: 0.30 (0.18), residues: 790 sheet: -0.54 (0.38), residues: 193 loop : -1.75 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 443 TYR 0.027 0.002 TYR B 705 PHE 0.021 0.002 PHE A 480 TRP 0.025 0.002 TRP A 368 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00335 (15270) covalent geometry : angle 0.61651 (20698) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.79458 ( 2) hydrogen bonds : bond 0.04663 ( 732) hydrogen bonds : angle 5.22535 ( 2012) Misc. bond : bond 0.00090 ( 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 271 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8199 (t80) cc_final: 0.7584 (t80) REVERT: A 317 TRP cc_start: 0.7543 (p-90) cc_final: 0.7182 (p90) REVERT: A 581 MET cc_start: 0.8760 (ttm) cc_final: 0.8530 (ttm) REVERT: A 668 ILE cc_start: 0.7049 (mt) cc_final: 0.6794 (mt) REVERT: A 670 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7355 (mm-40) REVERT: A 687 TYR cc_start: 0.6639 (m-80) cc_final: 0.6260 (m-80) REVERT: B 40 MET cc_start: 0.6756 (mtm) cc_final: 0.5916 (ttm) REVERT: B 165 ASP cc_start: 0.8388 (m-30) cc_final: 0.7943 (m-30) REVERT: B 181 ILE cc_start: 0.5170 (mm) cc_final: 0.4476 (mm) REVERT: B 227 MET cc_start: 0.6716 (ptt) cc_final: 0.5538 (mmp) REVERT: B 308 LYS cc_start: 0.8450 (mptt) cc_final: 0.7966 (mmmt) REVERT: B 392 ILE cc_start: 0.5324 (tp) cc_final: 0.4753 (tp) REVERT: B 479 LYS cc_start: 0.5685 (ptpp) cc_final: 0.5114 (mttt) REVERT: B 497 TYR cc_start: 0.7256 (t80) cc_final: 0.6979 (t80) REVERT: B 511 SER cc_start: 0.9180 (m) cc_final: 0.8891 (t) REVERT: B 557 TYR cc_start: 0.8774 (t80) cc_final: 0.8554 (t80) REVERT: B 654 ASN cc_start: 0.6031 (p0) cc_final: 0.4768 (t0) REVERT: B 664 HIS cc_start: 0.7627 (m-70) cc_final: 0.6940 (m-70) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3000 time to fit residues: 115.8550 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 : 0.607 ------------------------------------------------------------------------------- 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: 2.9990 chunk 130 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 167 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.200216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162670 restraints weight = 100487.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.170931 restraints weight = 50425.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.176331 restraints weight = 29240.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.179762 restraints weight = 19013.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.182133 restraints weight = 13755.946| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.8971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15272 Z= 0.232 Angle : 0.727 26.802 20700 Z= 0.395 Chirality : 0.043 0.256 2268 Planarity : 0.006 0.109 2586 Dihedral : 11.061 95.674 2310 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.19), residues: 1779 helix: -0.22 (0.17), residues: 789 sheet: -0.56 (0.38), residues: 199 loop : -1.89 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 230 TYR 0.032 0.003 TYR B 705 PHE 0.034 0.002 PHE B 344 TRP 0.034 0.003 TRP A 368 HIS 0.007 0.002 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00472 (15270) covalent geometry : angle 0.72679 (20698) SS BOND : bond 0.00336 ( 1) SS BOND : angle 1.73273 ( 2) hydrogen bonds : bond 0.05390 ( 732) hydrogen bonds : angle 5.73288 ( 2012) Misc. bond : bond 0.00146 ( 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 280 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8299 (t80) cc_final: 0.7658 (t80) REVERT: A 311 MET cc_start: -0.3197 (ptt) cc_final: -0.3433 (ptt) REVERT: A 392 GLN cc_start: 0.6230 (mt0) cc_final: 0.5464 (mt0) REVERT: A 410 GLU cc_start: 0.8822 (tt0) cc_final: 0.8528 (tt0) REVERT: A 548 MET cc_start: 0.5409 (mtp) cc_final: 0.5133 (mtp) REVERT: A 581 MET cc_start: 0.8956 (ttm) cc_final: 0.8444 (ttm) REVERT: A 668 ILE cc_start: 0.7449 (mt) cc_final: 0.7190 (mt) REVERT: B 40 MET cc_start: 0.6799 (mtm) cc_final: 0.6103 (ttm) REVERT: B 165 ASP cc_start: 0.8662 (m-30) cc_final: 0.8247 (m-30) REVERT: B 227 MET cc_start: 0.7039 (ptt) cc_final: 0.5788 (mmp) REVERT: B 392 ILE cc_start: 0.5465 (tp) cc_final: 0.4997 (tp) REVERT: B 479 LYS cc_start: 0.6269 (ptpp) cc_final: 0.5693 (mttt) REVERT: B 511 SER cc_start: 0.9248 (m) cc_final: 0.8857 (t) REVERT: B 517 ILE cc_start: 0.8200 (mp) cc_final: 0.7913 (mp) REVERT: B 654 ASN cc_start: 0.6530 (p0) cc_final: 0.5186 (t0) REVERT: B 664 HIS cc_start: 0.7728 (m-70) cc_final: 0.7219 (m-70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3148 time to fit residues: 124.3257 Evaluate side-chains 249 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 4.9990 chunk 153 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN F 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.204779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.167072 restraints weight = 99246.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.175408 restraints weight = 49537.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.180931 restraints weight = 28763.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.184128 restraints weight = 18701.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.186852 restraints weight = 13776.369| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.9110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15272 Z= 0.134 Angle : 0.614 26.851 20700 Z= 0.326 Chirality : 0.039 0.195 2268 Planarity : 0.004 0.051 2586 Dihedral : 10.787 95.168 2310 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.99 (0.19), residues: 1779 helix: 0.34 (0.18), residues: 788 sheet: -0.45 (0.38), residues: 197 loop : -1.74 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 151 TYR 0.024 0.002 TYR B 705 PHE 0.024 0.002 PHE B 94 TRP 0.018 0.002 TRP A 368 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00292 (15270) covalent geometry : angle 0.61371 (20698) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.87931 ( 2) hydrogen bonds : bond 0.04616 ( 732) hydrogen bonds : angle 5.17973 ( 2012) Misc. bond : bond 0.00149 ( 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 278 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.753 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: A 130 TYR cc_start: 0.8296 (t80) cc_final: 0.7687 (t80) REVERT: A 392 GLN cc_start: 0.6111 (mt0) cc_final: 0.5367 (mt0) REVERT: A 537 TRP cc_start: 0.7629 (m100) cc_final: 0.7218 (m100) REVERT: A 548 MET cc_start: 0.5199 (mtp) cc_final: 0.4876 (mtp) REVERT: A 581 MET cc_start: 0.8888 (ttm) cc_final: 0.8557 (ttm) REVERT: A 668 ILE cc_start: 0.7379 (mt) cc_final: 0.7133 (mt) REVERT: A 670 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7680 (mm-40) REVERT: B 40 MET cc_start: 0.6645 (mtm) cc_final: 0.5918 (ttm) REVERT: B 165 ASP cc_start: 0.8589 (m-30) cc_final: 0.8205 (m-30) REVERT: B 227 MET cc_start: 0.6985 (ptt) cc_final: 0.5728 (mmp) REVERT: B 392 ILE cc_start: 0.4994 (tp) cc_final: 0.4612 (tp) REVERT: B 479 LYS cc_start: 0.6210 (ptpp) cc_final: 0.5664 (mttt) REVERT: B 511 SER cc_start: 0.9223 (m) cc_final: 0.8872 (t) REVERT: B 654 ASN cc_start: 0.6718 (p0) cc_final: 0.5363 (t0) REVERT: B 664 HIS cc_start: 0.7554 (m-70) cc_final: 0.7261 (m-70) REVERT: C 51 MET cc_start: 0.8614 (mmm) cc_final: 0.8398 (mmt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2891 time to fit residues: 115.9791 Evaluate side-chains 249 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 7.9990 chunk 160 optimal weight: 0.5980 chunk 125 optimal weight: 0.0000 chunk 75 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 GLN B 629 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.205560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.167882 restraints weight = 95758.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.176464 restraints weight = 47185.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.182062 restraints weight = 26985.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.185743 restraints weight = 17366.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.188232 restraints weight = 12365.657| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.9180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15272 Z= 0.119 Angle : 0.594 26.807 20700 Z= 0.313 Chirality : 0.039 0.190 2268 Planarity : 0.004 0.044 2586 Dihedral : 10.669 95.080 2310 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -0.72 (0.20), residues: 1779 helix: 0.63 (0.18), residues: 787 sheet: -0.35 (0.38), residues: 191 loop : -1.65 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 213 TYR 0.019 0.002 TYR B 705 PHE 0.027 0.001 PHE C 119 TRP 0.018 0.001 TRP A 699 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00259 (15270) covalent geometry : angle 0.59366 (20698) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.57829 ( 2) hydrogen bonds : bond 0.04364 ( 732) hydrogen bonds : angle 4.96618 ( 2012) Misc. bond : bond 0.00146 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5021.03 seconds wall clock time: 86 minutes 20.72 seconds (5180.72 seconds total)