Starting phenix.real_space_refine on Fri Mar 6 06:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.map" model { file = "/net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj3_12371/03_2026/7nj3_12371.cif" } resolution = 4.48 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= 0.011 sd= 0.138 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 105 5.16 5 C 9307 2.51 5 N 2596 2.21 5 O 2879 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28778 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11704 Classifications: {'peptide': 735} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4075 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "F" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 729 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.16 Number of scatterers: 28778 At special positions: 0 Unit cell: (100.1, 105.6, 159.5, 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 105 16.00 P 23 15.00 O 2879 8.00 N 2596 7.00 C 9307 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 971.6 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: 75 helices and 17 sheets defined 49.6% alpha, 14.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.139A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.692A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.794A 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: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.634A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.971A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.827A 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: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.509A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A 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: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.236A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.584A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.618A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A 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: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A 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: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.174A 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: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.809A 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: 5.616A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 13 removed outlier: 5.836A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1989 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: 6.81 Time building geometry restraints manager: 3.96 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: 164 1.23 - 1.43: 6283 1.43 - 1.62: 8656 1.62 - 1.82: 181 Bond restraints: 29125 Sorted by residual: bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.519 -0.061 1.40e-02 5.10e+03 1.90e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" CD ARG F 98 " pdb=" NE ARG F 98 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA ARG F 71 " pdb=" C ARG F 71 " ideal model delta sigma weight residual 1.521 1.487 0.034 1.24e-02 6.50e+03 7.71e+00 ... (remaining 29120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 52261 5.64 - 11.28: 7 11.28 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 Bond angle restraints: 52274 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 79.81 28.19 3.00e+00 1.11e-01 8.83e+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 80.30 27.70 3.00e+00 1.11e-01 8.53e+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 82.46 26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.75 -26.85 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12555 17.94 - 35.88: 859 35.88 - 53.81: 257 53.81 - 71.75: 89 71.75 - 89.69: 16 Dihedral angle restraints: 13776 sinusoidal: 7725 harmonic: 6051 Sorted by residual: dihedral pdb=" N SER F 84 " pdb=" C SER F 84 " pdb=" CA SER F 84 " pdb=" CB SER F 84 " ideal model delta harmonic sigma weight residual 122.80 136.30 -13.50 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C SER F 84 " pdb=" N SER F 84 " pdb=" CA SER F 84 " pdb=" CB SER F 84 " ideal model delta harmonic sigma weight residual -122.60 -134.28 11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 13773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2180 0.099 - 0.199: 81 0.199 - 0.298: 4 0.298 - 0.397: 3 0.397 - 0.497: 1 Chirality restraints: 2269 Sorted by residual: chirality pdb=" CA SER F 84 " pdb=" N SER F 84 " pdb=" C SER F 84 " pdb=" CB SER F 84 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA THR F 24 " pdb=" N THR F 24 " pdb=" C THR F 24 " pdb=" CB THR F 24 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS F 64 " pdb=" N LYS F 64 " pdb=" C LYS F 64 " pdb=" CB LYS F 64 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2266 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.023 2.00e-02 2.50e+03 5.44e-02 5.92e+01 pdb=" CG TYR F 32 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.088 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " 0.084 2.00e-02 2.50e+03 4.40e-02 4.84e+01 pdb=" CG TRP F 112 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 59 " 0.027 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR F 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR F 59 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 59 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 59 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR F 59 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR F 59 " 0.046 2.00e-02 2.50e+03 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1259 2.17 - 2.78: 56211 2.78 - 3.39: 80883 3.39 - 3.99: 105788 3.99 - 4.60: 165140 Nonbonded interactions: 409281 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409276 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: 1.300 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: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 30.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3772 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15258 Z= 0.242 Angle : 0.703 26.846 20683 Z= 0.412 Chirality : 0.045 0.497 2269 Planarity : 0.005 0.076 2584 Dihedral : 14.398 89.690 5961 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.38 % Allowed : 0.44 % Favored : 99.18 % Cbeta Deviations : 0.06 % 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: -0.73 (0.19), residues: 1779 helix: 0.45 (0.19), residues: 786 sheet: -0.88 (0.35), residues: 193 loop : -1.29 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 71 TYR 0.088 0.003 TYR F 32 PHE 0.048 0.002 PHE A 446 TRP 0.084 0.002 TRP F 112 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00424 (15257) covalent geometry : angle 0.70155 (20681) SS BOND : bond 0.01513 ( 1) SS BOND : angle 5.12647 ( 2) hydrogen bonds : bond 0.15011 ( 731) hydrogen bonds : angle 5.85968 ( 2009) *********************** 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 422 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 416 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.1885 (mpp) cc_final: 0.1209 (mmt) REVERT: B 248 ILE cc_start: 0.7981 (tt) cc_final: 0.7502 (tt) REVERT: B 317 MET cc_start: 0.7206 (mmm) cc_final: 0.6531 (mmm) REVERT: C 232 LEU cc_start: 0.6244 (tp) cc_final: 0.5476 (tt) REVERT: C 243 MET cc_start: -0.1972 (mtt) cc_final: -0.3321 (tmm) REVERT: F 32 TYR cc_start: 0.3678 (m-80) cc_final: 0.3444 (p90) REVERT: F 59 TYR cc_start: 0.5504 (m-80) cc_final: 0.4920 (m-80) outliers start: 6 outliers final: 0 residues processed: 419 average time/residue: 0.3415 time to fit residues: 196.4458 Evaluate side-chains 273 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A 703 ASN B 134 ASN B 310 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.216216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.171167 restraints weight = 102058.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.178892 restraints weight = 50576.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.183578 restraints weight = 30853.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.186931 restraints weight = 22378.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.188461 restraints weight = 17991.700| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5165 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15258 Z= 0.259 Angle : 0.692 27.318 20683 Z= 0.372 Chirality : 0.041 0.184 2269 Planarity : 0.005 0.051 2584 Dihedral : 10.293 73.279 2310 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.88 (0.19), residues: 1779 helix: 0.20 (0.18), residues: 800 sheet: -0.67 (0.36), residues: 188 loop : -1.32 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 124 TYR 0.016 0.002 TYR A 650 PHE 0.026 0.002 PHE F 47 TRP 0.016 0.002 TRP F 112 HIS 0.008 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00504 (15257) covalent geometry : angle 0.69174 (20681) SS BOND : bond 0.08564 ( 1) SS BOND : angle 2.70389 ( 2) hydrogen bonds : bond 0.05612 ( 731) hydrogen bonds : angle 5.33947 ( 2009) *********************** 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 311 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.734 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: A 258 GLU cc_start: 0.7173 (tp30) cc_final: 0.6724 (tp30) REVERT: A 272 ASP cc_start: 0.8175 (m-30) cc_final: 0.7654 (t70) REVERT: A 628 VAL cc_start: 0.5946 (t) cc_final: 0.5698 (t) REVERT: B 2 ASP cc_start: 0.8087 (m-30) cc_final: 0.7409 (m-30) REVERT: B 248 ILE cc_start: 0.8970 (tt) cc_final: 0.8665 (mm) REVERT: B 408 MET cc_start: 0.5999 (tpt) cc_final: 0.5541 (tpt) REVERT: B 411 MET cc_start: 0.8199 (mmm) cc_final: 0.7682 (mmm) REVERT: C 243 MET cc_start: -0.2220 (mtt) cc_final: -0.3256 (tmm) REVERT: F 98 ARG cc_start: 0.2372 (mmt180) cc_final: 0.1846 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3132 time to fit residues: 137.0842 Evaluate side-chains 262 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 65 GLN B 292 ASN B 346 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 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 = 0.4792 r_free = 0.4792 target = 0.209187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.163098 restraints weight = 103547.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.170198 restraints weight = 52291.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.174790 restraints weight = 32808.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.177837 restraints weight = 24068.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.179391 restraints weight = 19716.752| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15258 Z= 0.191 Angle : 0.627 25.482 20683 Z= 0.336 Chirality : 0.039 0.196 2269 Planarity : 0.005 0.055 2584 Dihedral : 10.200 73.283 2310 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.78 % 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: -0.87 (0.19), residues: 1779 helix: 0.26 (0.18), residues: 805 sheet: -0.74 (0.34), residues: 214 loop : -1.38 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.021 0.002 TYR F 94 PHE 0.019 0.002 PHE A 503 TRP 0.024 0.002 TRP F 112 HIS 0.006 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00418 (15257) covalent geometry : angle 0.62675 (20681) SS BOND : bond 0.00537 ( 1) SS BOND : angle 1.01284 ( 2) hydrogen bonds : bond 0.05003 ( 731) hydrogen bonds : angle 5.11688 ( 2009) *********************** 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 303 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.716 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 47 MET cc_start: 0.1703 (tpt) cc_final: 0.1147 (ptt) REVERT: A 258 GLU cc_start: 0.7156 (tp30) cc_final: 0.6837 (tp30) REVERT: A 272 ASP cc_start: 0.8142 (m-30) cc_final: 0.7757 (p0) REVERT: A 431 ASP cc_start: 0.7234 (p0) cc_final: 0.6991 (p0) REVERT: A 469 LEU cc_start: 0.5105 (tp) cc_final: 0.4849 (mm) REVERT: A 486 ILE cc_start: 0.8573 (mm) cc_final: 0.8336 (mm) REVERT: B 150 PHE cc_start: 0.9187 (m-80) cc_final: 0.8912 (m-80) REVERT: B 246 MET cc_start: 0.7691 (mpp) cc_final: 0.7014 (mtm) REVERT: B 248 ILE cc_start: 0.8901 (tt) cc_final: 0.8550 (mm) REVERT: B 460 GLN cc_start: 0.5376 (tt0) cc_final: 0.5074 (tt0) REVERT: B 481 LYS cc_start: 0.8838 (mttm) cc_final: 0.7985 (tppt) REVERT: B 621 GLN cc_start: 0.7579 (tt0) cc_final: 0.7367 (tt0) REVERT: C 232 LEU cc_start: 0.7069 (tp) cc_final: 0.6729 (tt) REVERT: C 243 MET cc_start: -0.1911 (mtt) cc_final: -0.3004 (tmm) outliers start: 2 outliers final: 0 residues processed: 303 average time/residue: 0.2927 time to fit residues: 127.0776 Evaluate side-chains 250 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 294 GLN B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 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 = 0.4733 r_free = 0.4733 target = 0.203296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.161382 restraints weight = 100866.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.165347 restraints weight = 59611.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.167817 restraints weight = 40739.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.169171 restraints weight = 30850.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.169660 restraints weight = 28413.385| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15258 Z= 0.205 Angle : 0.659 28.524 20683 Z= 0.349 Chirality : 0.040 0.169 2269 Planarity : 0.005 0.068 2584 Dihedral : 10.247 76.016 2310 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1779 helix: 0.24 (0.18), residues: 806 sheet: -1.00 (0.34), residues: 214 loop : -1.60 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 116 TYR 0.021 0.002 TYR A 650 PHE 0.021 0.002 PHE A 411 TRP 0.015 0.002 TRP A 577 HIS 0.013 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00445 (15257) covalent geometry : angle 0.65891 (20681) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.43360 ( 2) hydrogen bonds : bond 0.05083 ( 731) hydrogen bonds : angle 5.17610 ( 2009) *********************** 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 287 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.668 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: A 47 MET cc_start: 0.0985 (tpt) cc_final: 0.0671 (ptt) REVERT: A 431 ASP cc_start: 0.7768 (p0) cc_final: 0.7477 (p0) REVERT: A 486 ILE cc_start: 0.8649 (mm) cc_final: 0.8407 (mm) REVERT: B 150 PHE cc_start: 0.9296 (m-80) cc_final: 0.9016 (m-80) REVERT: B 246 MET cc_start: 0.7394 (mpp) cc_final: 0.7021 (mtm) REVERT: B 321 MET cc_start: 0.8677 (mtt) cc_final: 0.8451 (mtt) REVERT: B 411 MET cc_start: 0.8458 (mmm) cc_final: 0.8119 (mmm) REVERT: B 460 GLN cc_start: 0.5684 (tt0) cc_final: 0.5382 (tt0) REVERT: B 481 LYS cc_start: 0.8821 (mttm) cc_final: 0.8137 (tppt) REVERT: C 210 GLU cc_start: 0.7231 (tt0) cc_final: 0.6699 (mm-30) REVERT: C 243 MET cc_start: -0.1300 (mtt) cc_final: -0.2491 (tmm) REVERT: F 86 LYS cc_start: 0.6981 (mttt) cc_final: 0.6614 (mmtp) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.3037 time to fit residues: 123.2350 Evaluate side-chains 233 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.0000 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN B 634 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN F 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.206078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.160893 restraints weight = 101936.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.167490 restraints weight = 52755.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.171844 restraints weight = 33473.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.174702 restraints weight = 24877.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.176086 restraints weight = 20587.865| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15258 Z= 0.118 Angle : 0.555 26.532 20683 Z= 0.290 Chirality : 0.038 0.169 2269 Planarity : 0.005 0.094 2584 Dihedral : 10.125 77.855 2310 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1779 helix: 0.73 (0.18), residues: 794 sheet: -0.84 (0.35), residues: 215 loop : -1.52 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 124 TYR 0.012 0.001 TYR B 599 PHE 0.016 0.001 PHE B 495 TRP 0.016 0.001 TRP A 317 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00256 (15257) covalent geometry : angle 0.55514 (20681) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.50972 ( 2) hydrogen bonds : bond 0.04313 ( 731) hydrogen bonds : angle 4.78108 ( 2009) *********************** 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 282 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.694 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: A 1 MET cc_start: -0.0251 (tmm) cc_final: -0.1552 (tpt) REVERT: A 486 ILE cc_start: 0.8456 (mm) cc_final: 0.8231 (mm) REVERT: A 539 LYS cc_start: 0.8732 (mttp) cc_final: 0.8367 (mttp) REVERT: B 150 PHE cc_start: 0.9206 (m-80) cc_final: 0.8927 (m-80) REVERT: B 246 MET cc_start: 0.7355 (mpp) cc_final: 0.6828 (mtm) REVERT: B 321 MET cc_start: 0.8709 (mtt) cc_final: 0.8428 (mtt) REVERT: B 411 MET cc_start: 0.8243 (mmm) cc_final: 0.7902 (mmm) REVERT: B 460 GLN cc_start: 0.5730 (tt0) cc_final: 0.5416 (tt0) REVERT: B 481 LYS cc_start: 0.8778 (mttm) cc_final: 0.8064 (tppt) REVERT: B 534 MET cc_start: 0.3986 (tpt) cc_final: 0.3782 (tpt) REVERT: C 210 GLU cc_start: 0.7140 (tt0) cc_final: 0.6668 (mm-30) REVERT: C 243 MET cc_start: -0.1436 (mtt) cc_final: -0.2632 (tmm) REVERT: F 18 LEU cc_start: 0.8900 (tp) cc_final: 0.8516 (tt) REVERT: F 86 LYS cc_start: 0.6874 (mttt) cc_final: 0.6509 (mmtp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2916 time to fit residues: 118.0259 Evaluate side-chains 235 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 chunk 174 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 425 ASN B 605 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 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 = 0.4748 r_free = 0.4748 target = 0.205276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160401 restraints weight = 98948.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.167097 restraints weight = 50505.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.171481 restraints weight = 31878.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.174465 restraints weight = 23558.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175734 restraints weight = 19371.571| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15258 Z= 0.119 Angle : 0.543 27.043 20683 Z= 0.283 Chirality : 0.037 0.147 2269 Planarity : 0.004 0.043 2584 Dihedral : 10.068 81.461 2310 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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: -0.49 (0.19), residues: 1779 helix: 0.89 (0.18), residues: 798 sheet: -0.74 (0.36), residues: 212 loop : -1.50 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 124 TYR 0.011 0.001 TYR A 650 PHE 0.021 0.001 PHE A 446 TRP 0.009 0.001 TRP A 577 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00260 (15257) covalent geometry : angle 0.54286 (20681) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.49600 ( 2) hydrogen bonds : bond 0.04105 ( 731) hydrogen bonds : angle 4.65934 ( 2009) *********************** 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 276 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.0606 (tmm) cc_final: -0.1843 (tpt) REVERT: A 486 ILE cc_start: 0.8431 (mm) cc_final: 0.8182 (mm) REVERT: B 150 PHE cc_start: 0.9126 (m-80) cc_final: 0.8853 (m-80) REVERT: B 246 MET cc_start: 0.7408 (mpp) cc_final: 0.6858 (mtm) REVERT: B 321 MET cc_start: 0.8733 (mtt) cc_final: 0.8440 (mtt) REVERT: B 411 MET cc_start: 0.8341 (mmm) cc_final: 0.7841 (mmm) REVERT: B 460 GLN cc_start: 0.5779 (tt0) cc_final: 0.5459 (tt0) REVERT: B 481 LYS cc_start: 0.8773 (mttm) cc_final: 0.8041 (tppt) REVERT: B 534 MET cc_start: 0.4009 (tpt) cc_final: 0.3727 (tpt) REVERT: B 621 GLN cc_start: 0.7563 (tt0) cc_final: 0.7350 (tt0) REVERT: C 51 MET cc_start: 0.6966 (mmm) cc_final: 0.6544 (mmm) REVERT: C 210 GLU cc_start: 0.7075 (tt0) cc_final: 0.6674 (mm-30) REVERT: C 243 MET cc_start: -0.1441 (mtt) cc_final: -0.2644 (tmm) REVERT: F 18 LEU cc_start: 0.8674 (tp) cc_final: 0.8394 (tt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2940 time to fit residues: 115.2936 Evaluate side-chains 231 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 151 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 99 HIS B 328 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 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 = 0.4665 r_free = 0.4665 target = 0.195996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.148831 restraints weight = 103089.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155267 restraints weight = 52792.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.159486 restraints weight = 33676.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.162234 restraints weight = 25267.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.163569 restraints weight = 21173.071| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15258 Z= 0.220 Angle : 0.673 24.902 20683 Z= 0.360 Chirality : 0.040 0.151 2269 Planarity : 0.005 0.052 2584 Dihedral : 10.447 87.524 2310 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.04 (0.19), residues: 1779 helix: 0.35 (0.17), residues: 811 sheet: -0.85 (0.37), residues: 202 loop : -1.76 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.020 0.002 TYR A 650 PHE 0.031 0.002 PHE A 411 TRP 0.014 0.002 TRP A 619 HIS 0.011 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00468 (15257) covalent geometry : angle 0.67305 (20681) SS BOND : bond 0.00254 ( 1) SS BOND : angle 0.86549 ( 2) hydrogen bonds : bond 0.05177 ( 731) hydrogen bonds : angle 5.24457 ( 2009) *********************** 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 275 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0052 (tmm) cc_final: -0.1287 (tpt) REVERT: A 272 ASP cc_start: 0.8105 (p0) cc_final: 0.7849 (p0) REVERT: A 285 MET cc_start: 0.8729 (tpt) cc_final: 0.8118 (tpt) REVERT: A 374 MET cc_start: 0.7871 (mmm) cc_final: 0.7524 (mmm) REVERT: A 390 LEU cc_start: 0.8204 (tp) cc_final: 0.7978 (tp) REVERT: A 431 ASP cc_start: 0.7682 (p0) cc_final: 0.7481 (p0) REVERT: B 150 PHE cc_start: 0.9107 (m-80) cc_final: 0.8827 (m-80) REVERT: B 246 MET cc_start: 0.7624 (mpp) cc_final: 0.7249 (mtp) REVERT: B 321 MET cc_start: 0.8750 (mtt) cc_final: 0.8456 (mtt) REVERT: B 408 MET cc_start: 0.6288 (tpt) cc_final: 0.6075 (tpp) REVERT: B 411 MET cc_start: 0.8536 (mmm) cc_final: 0.7982 (mmm) REVERT: B 460 GLN cc_start: 0.6330 (tt0) cc_final: 0.6084 (tt0) REVERT: B 478 SER cc_start: 0.8482 (t) cc_final: 0.8136 (t) REVERT: B 481 LYS cc_start: 0.8885 (mttm) cc_final: 0.8229 (tppt) REVERT: B 534 MET cc_start: 0.3981 (tpt) cc_final: 0.3734 (tpt) REVERT: B 621 GLN cc_start: 0.7664 (tt0) cc_final: 0.7400 (tt0) REVERT: C 243 MET cc_start: -0.1255 (mtt) cc_final: -0.2354 (tmm) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2918 time to fit residues: 115.0171 Evaluate side-chains 232 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 537 ASN C 137 ASN ** F 117 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 = 0.4710 r_free = 0.4710 target = 0.200156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.156681 restraints weight = 104191.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.161339 restraints weight = 55242.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164938 restraints weight = 39275.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.167232 restraints weight = 28122.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.167449 restraints weight = 23773.756| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15258 Z= 0.114 Angle : 0.560 27.571 20683 Z= 0.292 Chirality : 0.038 0.157 2269 Planarity : 0.005 0.097 2584 Dihedral : 10.320 89.821 2310 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.37 % 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: -0.64 (0.19), residues: 1779 helix: 0.81 (0.18), residues: 812 sheet: -0.91 (0.38), residues: 195 loop : -1.65 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.015 0.001 TYR A 650 PHE 0.026 0.002 PHE A 205 TRP 0.012 0.001 TRP F 36 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00252 (15257) covalent geometry : angle 0.56041 (20681) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.55865 ( 2) hydrogen bonds : bond 0.04161 ( 731) hydrogen bonds : angle 4.77534 ( 2009) *********************** 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 279 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.0229 (tmm) cc_final: -0.0757 (tpt) REVERT: A 272 ASP cc_start: 0.7999 (p0) cc_final: 0.7780 (p0) REVERT: A 374 MET cc_start: 0.7852 (mmm) cc_final: 0.7527 (mmm) REVERT: A 431 ASP cc_start: 0.7714 (p0) cc_final: 0.7428 (p0) REVERT: B 150 PHE cc_start: 0.9060 (m-80) cc_final: 0.8756 (m-80) REVERT: B 246 MET cc_start: 0.7528 (mpp) cc_final: 0.7107 (mtp) REVERT: B 395 LEU cc_start: 0.9146 (mp) cc_final: 0.8936 (mp) REVERT: B 411 MET cc_start: 0.8369 (mmm) cc_final: 0.7858 (mmm) REVERT: B 460 GLN cc_start: 0.6257 (tt0) cc_final: 0.6014 (tt0) REVERT: B 481 LYS cc_start: 0.8818 (mttm) cc_final: 0.7955 (tppt) REVERT: B 504 ASN cc_start: 0.5058 (m-40) cc_final: 0.4599 (m110) REVERT: B 534 MET cc_start: 0.3828 (tpt) cc_final: 0.3618 (tpt) REVERT: C 51 MET cc_start: 0.7241 (mmm) cc_final: 0.6844 (mmm) REVERT: C 243 MET cc_start: -0.1178 (mtt) cc_final: -0.2264 (tmm) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.2777 time to fit residues: 112.6627 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** F 117 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 = 0.4663 r_free = 0.4663 target = 0.196177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.151204 restraints weight = 102357.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.157307 restraints weight = 56555.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.159492 restraints weight = 38156.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.161687 restraints weight = 30324.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.161827 restraints weight = 26324.291| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15258 Z= 0.169 Angle : 0.596 26.594 20683 Z= 0.317 Chirality : 0.038 0.150 2269 Planarity : 0.005 0.099 2584 Dihedral : 10.443 93.736 2310 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1779 helix: 0.71 (0.18), residues: 812 sheet: -0.93 (0.37), residues: 205 loop : -1.75 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.017 0.002 TYR A 650 PHE 0.022 0.002 PHE A 520 TRP 0.012 0.002 TRP B 438 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00361 (15257) covalent geometry : angle 0.59580 (20681) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.95367 ( 2) hydrogen bonds : bond 0.04591 ( 731) hydrogen bonds : angle 5.05440 ( 2009) *********************** 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 277 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.745 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: A 1 MET cc_start: -0.0067 (tmm) cc_final: -0.1435 (tpt) REVERT: A 374 MET cc_start: 0.7796 (mmm) cc_final: 0.7457 (mmm) REVERT: A 390 LEU cc_start: 0.8352 (tp) cc_final: 0.8148 (tp) REVERT: A 431 ASP cc_start: 0.7846 (p0) cc_final: 0.7589 (p0) REVERT: A 460 MET cc_start: 0.7907 (mmt) cc_final: 0.6996 (mmt) REVERT: A 629 GLU cc_start: 0.4324 (mm-30) cc_final: 0.3714 (mp0) REVERT: B 150 PHE cc_start: 0.9061 (m-80) cc_final: 0.8755 (m-80) REVERT: B 246 MET cc_start: 0.7670 (mpp) cc_final: 0.7237 (mtp) REVERT: B 395 LEU cc_start: 0.9165 (mp) cc_final: 0.8945 (mp) REVERT: B 408 MET cc_start: 0.6258 (tpt) cc_final: 0.5749 (tpp) REVERT: B 411 MET cc_start: 0.8543 (mmm) cc_final: 0.7912 (mmm) REVERT: B 534 MET cc_start: 0.4054 (tpt) cc_final: 0.3803 (tpt) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.2799 time to fit residues: 113.1640 Evaluate side-chains 234 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 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 42 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.0060 chunk 98 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN B 460 GLN C 134 HIS C 137 ASN ** F 117 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 = 0.4682 r_free = 0.4682 target = 0.197408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.153333 restraints weight = 102016.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.158919 restraints weight = 55526.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.160879 restraints weight = 40344.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.162870 restraints weight = 31708.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.163444 restraints weight = 26848.135| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.7609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15258 Z= 0.119 Angle : 0.560 26.825 20683 Z= 0.293 Chirality : 0.038 0.148 2269 Planarity : 0.005 0.086 2584 Dihedral : 10.392 95.255 2310 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1779 helix: 0.85 (0.18), residues: 812 sheet: -0.84 (0.39), residues: 188 loop : -1.70 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 716 TYR 0.014 0.001 TYR A 650 PHE 0.018 0.001 PHE A 520 TRP 0.011 0.001 TRP F 36 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00262 (15257) covalent geometry : angle 0.56038 (20681) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.55054 ( 2) hydrogen bonds : bond 0.04150 ( 731) hydrogen bonds : angle 4.83676 ( 2009) ********************** 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 274 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.665 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: A 1 MET cc_start: -0.0075 (tmm) cc_final: -0.1397 (tpt) REVERT: A 374 MET cc_start: 0.7721 (mmm) cc_final: 0.7398 (mmm) REVERT: A 390 LEU cc_start: 0.8356 (tp) cc_final: 0.8143 (tp) REVERT: A 431 ASP cc_start: 0.7732 (p0) cc_final: 0.7452 (p0) REVERT: A 629 GLU cc_start: 0.4198 (mm-30) cc_final: 0.3702 (mp0) REVERT: B 150 PHE cc_start: 0.9000 (m-80) cc_final: 0.8699 (m-80) REVERT: B 289 MET cc_start: 0.6785 (ttt) cc_final: 0.6524 (ttm) REVERT: B 395 LEU cc_start: 0.9171 (mp) cc_final: 0.8950 (mp) REVERT: B 411 MET cc_start: 0.8492 (mmm) cc_final: 0.7797 (mmm) REVERT: B 534 MET cc_start: 0.3815 (tpt) cc_final: 0.3585 (tpt) REVERT: C 243 MET cc_start: -0.0928 (mtt) cc_final: -0.2028 (tmm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2730 time to fit residues: 108.9516 Evaluate side-chains 235 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 73 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN B 537 ASN B 676 ASN C 137 ASN ** F 117 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 = 0.4659 r_free = 0.4659 target = 0.195292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.151826 restraints weight = 105467.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.154803 restraints weight = 59323.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.158737 restraints weight = 46621.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.160408 restraints weight = 33062.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.161165 restraints weight = 28437.114| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15258 Z= 0.142 Angle : 0.581 26.694 20683 Z= 0.306 Chirality : 0.038 0.148 2269 Planarity : 0.005 0.086 2584 Dihedral : 10.462 97.382 2310 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % 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: -0.70 (0.19), residues: 1779 helix: 0.81 (0.18), residues: 811 sheet: -0.85 (0.37), residues: 204 loop : -1.76 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 716 TYR 0.024 0.002 TYR B 620 PHE 0.018 0.002 PHE A 520 TRP 0.010 0.001 TRP A 577 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00308 (15257) covalent geometry : angle 0.58146 (20681) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.62816 ( 2) hydrogen bonds : bond 0.04303 ( 731) hydrogen bonds : angle 4.88802 ( 2009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5570.46 seconds wall clock time: 95 minutes 28.11 seconds (5728.11 seconds total)