Starting phenix.real_space_refine on Sun Jul 5 16:12:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nj7_12375/07_2026/7nj7_12375.cif" } resolution = 4.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.261 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 106 5.16 5 C 9336 2.51 5 N 2604 2.21 5 O 2881 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28818 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: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 3 Time building chain proxies: 5.03, per 1000 atoms: 0.17 Number of scatterers: 28818 At special positions: 0 Unit cell: (102, 112, 174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 23 15.00 O 2881 8.00 N 2604 7.00 C 9336 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 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: 2.93 Conformation dependent library (CDL) restraints added in 653.1 milliseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 18 sheets defined 49.7% alpha, 14.2% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.692A 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: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A 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: 3.588A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.330A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.977A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.108A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A 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: 3.747A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A 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 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.537A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.599A 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: 11.690A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.929A 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: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.174A 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: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A 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 10 through 11 removed outlier: 6.836A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 98 727 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 3.75 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: 426 1.23 - 1.43: 6047 1.43 - 1.63: 8669 1.63 - 1.83: 183 Bond restraints: 29166 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.511 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" CD ARG F 61 " pdb=" NE ARG F 61 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" CD ARG F 72 " pdb=" NE ARG F 72 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CD ARG F 50 " pdb=" NE ARG F 50 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.97e+00 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.84e+00 ... (remaining 29161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 52308 5.64 - 11.27: 15 11.27 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 Bond angle restraints: 52329 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 80.32 27.68 3.00e+00 1.11e-01 8.52e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.81 27.19 3.00e+00 1.11e-01 8.22e+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 82.44 26.56 3.00e+00 1.11e-01 7.84e+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 52324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12544 17.94 - 35.88: 856 35.88 - 53.83: 244 53.83 - 71.77: 68 71.77 - 89.71: 12 Dihedral angle restraints: 13724 sinusoidal: 7661 harmonic: 6063 Sorted by residual: dihedral pdb=" CA ALA F 35 " pdb=" C ALA F 35 " pdb=" N TRP F 36 " pdb=" CA TRP F 36 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ARG F 72 " pdb=" C ARG F 72 " pdb=" N ASP F 73 " pdb=" CA ASP F 73 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS F 76 " pdb=" C LYS F 76 " pdb=" N ASN F 77 " pdb=" CA ASN F 77 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1880 0.050 - 0.100: 295 0.100 - 0.149: 75 0.149 - 0.199: 20 0.199 - 0.249: 6 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA VAL F 2 " pdb=" N VAL F 2 " pdb=" C VAL F 2 " pdb=" CB VAL F 2 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU F 51 " pdb=" N LEU F 51 " pdb=" C LEU F 51 " pdb=" CB LEU F 51 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2273 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 38 " -0.475 9.50e-02 1.11e+02 2.13e-01 2.83e+01 pdb=" NE ARG F 38 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 38 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG F 38 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 38 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 68 " 0.057 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE F 68 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 68 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE F 68 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE F 68 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 68 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 68 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 95 " 0.062 2.00e-02 2.50e+03 3.22e-02 2.07e+01 pdb=" CG TYR F 95 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 95 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR F 95 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR F 95 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 95 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 95 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 95 " 0.041 2.00e-02 2.50e+03 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1260 2.17 - 2.78: 56237 2.78 - 3.39: 80883 3.39 - 3.99: 105856 3.99 - 4.60: 165095 Nonbonded interactions: 409331 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 1.569 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.160 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4589 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 0.054 15299 Z= 0.236 Angle : 0.727 26.848 20738 Z= 0.430 Chirality : 0.044 0.249 2276 Planarity : 0.007 0.213 2590 Dihedral : 13.692 89.712 5908 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % 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: -0.72 (0.19), residues: 1781 helix: 0.46 (0.19), residues: 786 sheet: -0.72 (0.36), residues: 188 loop : -1.31 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 72 TYR 0.062 0.002 TYR F 95 PHE 0.057 0.002 PHE F 68 TRP 0.030 0.002 TRP F 36 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.24 (15298) covalent geometry : angle 0.72724 / 0.43 (20736) SS BOND : bond 0.01177 / 0.56 ( 1) SS BOND : angle 1.92260 / 1.11 ( 2) hydrogen bonds : bond 0.14986 / 9.67 ( 732) hydrogen bonds : angle 5.89777 / 4.24 ( 2006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 365 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 362 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 PHE cc_start: 0.6581 (t80) cc_final: 0.6232 (t80) REVERT: A 282 PHE cc_start: 0.7150 (p90) cc_final: 0.6681 (p90) REVERT: A 334 TYR cc_start: 0.7534 (m-80) cc_final: 0.6599 (m-10) REVERT: A 483 ILE cc_start: 0.8212 (mt) cc_final: 0.8008 (tp) REVERT: A 545 ILE cc_start: 0.5896 (pt) cc_final: 0.5618 (pt) REVERT: A 581 MET cc_start: 0.7677 (mtp) cc_final: 0.6784 (mtp) REVERT: A 585 LEU cc_start: 0.7686 (mt) cc_final: 0.7309 (tp) REVERT: A 648 SER cc_start: 0.9248 (t) cc_final: 0.9038 (m) REVERT: A 667 LEU cc_start: 0.8988 (mt) cc_final: 0.8472 (mt) REVERT: B 223 THR cc_start: 0.7027 (t) cc_final: 0.6775 (t) REVERT: B 236 LEU cc_start: 0.8817 (tp) cc_final: 0.8510 (pt) REVERT: B 261 SER cc_start: 0.8474 (m) cc_final: 0.8251 (p) REVERT: B 519 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7423 (tt0) REVERT: B 609 VAL cc_start: 0.7594 (t) cc_final: 0.7263 (t) REVERT: B 657 TYR cc_start: 0.8327 (p90) cc_final: 0.7371 (p90) REVERT: C 49 TRP cc_start: 0.7612 (t-100) cc_final: 0.7081 (t60) REVERT: C 90 MET cc_start: 0.3848 (mtm) cc_final: 0.3602 (ptp) REVERT: C 192 GLU cc_start: 0.7970 (tp30) cc_final: 0.7618 (tp30) REVERT: C 232 LEU cc_start: 0.6663 (tp) cc_final: 0.6136 (tt) REVERT: C 240 TRP cc_start: 0.6411 (p-90) cc_final: 0.5866 (p-90) outliers start: 3 outliers final: 1 residues processed: 365 average time/residue: 0.3076 time to fit residues: 158.5616 Evaluate side-chains 256 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN B 756 GLN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.127909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.108559 restraints weight = 195828.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.113644 restraints weight = 101578.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.116852 restraints weight = 58691.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.118914 restraints weight = 37645.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.120124 restraints weight = 26399.201| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15299 Z= 0.186 Angle : 0.633 27.547 20738 Z= 0.339 Chirality : 0.039 0.241 2276 Planarity : 0.005 0.060 2590 Dihedral : 6.866 63.074 2235 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1781 helix: 0.42 (0.18), residues: 786 sheet: -0.40 (0.38), residues: 191 loop : -1.24 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 572 TYR 0.020 0.002 TYR B 49 PHE 0.031 0.002 PHE A 446 TRP 0.015 0.002 TRP B 613 HIS 0.008 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (15298) covalent geometry : angle 0.63311 / 0.34 (20736) SS BOND : bond 0.00614 / 0.29 ( 1) SS BOND : angle 2.13321 / 1.23 ( 2) hydrogen bonds : bond 0.04841 / 3.12 ( 732) hydrogen bonds : angle 5.03261 / 3.61 ( 2006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 291 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.0222 (ppp) cc_final: -0.0127 (ppp) REVERT: A 260 PHE cc_start: 0.7484 (t80) cc_final: 0.6573 (t80) REVERT: A 459 ILE cc_start: 0.5738 (mt) cc_final: 0.5242 (mt) REVERT: A 477 MET cc_start: 0.4683 (mtp) cc_final: 0.4225 (ptp) REVERT: A 579 MET cc_start: 0.8687 (tmm) cc_final: 0.7750 (ttt) REVERT: A 581 MET cc_start: 0.8473 (mtp) cc_final: 0.7533 (mtp) REVERT: A 585 LEU cc_start: 0.7725 (mt) cc_final: 0.7437 (tp) REVERT: A 661 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 40 MET cc_start: 0.8672 (mtp) cc_final: 0.7851 (ttp) REVERT: B 179 MET cc_start: 0.1616 (mtt) cc_final: 0.0502 (mtt) REVERT: B 317 MET cc_start: 0.8803 (ttm) cc_final: 0.8069 (tpp) REVERT: B 389 ILE cc_start: 0.8728 (mt) cc_final: 0.8291 (mt) REVERT: B 620 TYR cc_start: 0.7272 (t80) cc_final: 0.5737 (t80) REVERT: B 657 TYR cc_start: 0.8530 (p90) cc_final: 0.7904 (p90) REVERT: B 688 MET cc_start: 0.8775 (mmp) cc_final: 0.8530 (mmm) REVERT: B 744 MET cc_start: 0.5010 (ptm) cc_final: 0.4762 (ppp) REVERT: C 49 TRP cc_start: 0.8987 (t-100) cc_final: 0.8011 (t60) REVERT: C 50 MET cc_start: 0.8485 (ptm) cc_final: 0.7915 (tpp) REVERT: C 90 MET cc_start: 0.5069 (mtm) cc_final: 0.4556 (ptt) REVERT: C 170 ASN cc_start: 0.7474 (m-40) cc_final: 0.7239 (m110) REVERT: F 34 MET cc_start: -0.2533 (mmt) cc_final: -0.3703 (tmm) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3010 time to fit residues: 125.8920 Evaluate side-chains 234 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 27 optimal weight: 0.0970 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 425 ASN B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.127727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.108500 restraints weight = 195682.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.113523 restraints weight = 100792.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.116693 restraints weight = 58074.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.118588 restraints weight = 37135.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.119983 restraints weight = 26605.710| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15299 Z= 0.118 Angle : 0.539 26.109 20738 Z= 0.283 Chirality : 0.038 0.156 2276 Planarity : 0.005 0.101 2590 Dihedral : 6.663 66.133 2235 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % 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: -0.43 (0.19), residues: 1781 helix: 0.61 (0.18), residues: 797 sheet: -0.27 (0.38), residues: 191 loop : -1.19 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 151 TYR 0.012 0.001 TYR B 217 PHE 0.019 0.001 PHE A 446 TRP 0.008 0.001 TRP F 115 HIS 0.011 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15298) covalent geometry : angle 0.53853 / 0.28 (20736) SS BOND : bond 0.00270 / 0.13 ( 1) SS BOND : angle 1.03619 / 0.60 ( 2) hydrogen bonds : bond 0.04158 / 2.68 ( 732) hydrogen bonds : angle 4.76059 / 3.41 ( 2006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 266 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.0247 (ppp) cc_final: -0.0042 (ppp) REVERT: A 150 PHE cc_start: 0.5305 (m-80) cc_final: 0.3932 (m-80) REVERT: A 260 PHE cc_start: 0.7376 (t80) cc_final: 0.6465 (t80) REVERT: A 459 ILE cc_start: 0.6453 (mt) cc_final: 0.5482 (mt) REVERT: A 579 MET cc_start: 0.7863 (tmm) cc_final: 0.7561 (ttt) REVERT: A 581 MET cc_start: 0.8364 (mtp) cc_final: 0.7436 (mtp) REVERT: A 585 LEU cc_start: 0.7846 (mt) cc_final: 0.7092 (tp) REVERT: B 40 MET cc_start: 0.8715 (mtp) cc_final: 0.8059 (ttm) REVERT: B 222 LEU cc_start: 0.8448 (mm) cc_final: 0.8024 (mm) REVERT: B 347 LYS cc_start: 0.8661 (pttm) cc_final: 0.8206 (tptp) REVERT: B 348 MET cc_start: 0.5454 (mmp) cc_final: 0.4355 (mmt) REVERT: B 389 ILE cc_start: 0.8768 (mt) cc_final: 0.8551 (mt) REVERT: B 403 LEU cc_start: 0.9237 (tp) cc_final: 0.9017 (pp) REVERT: B 407 MET cc_start: 0.8461 (tpp) cc_final: 0.7977 (tpp) REVERT: B 411 MET cc_start: 0.8054 (mmm) cc_final: 0.7134 (mmm) REVERT: B 620 TYR cc_start: 0.6972 (t80) cc_final: 0.5324 (t80) REVERT: B 657 TYR cc_start: 0.8619 (p90) cc_final: 0.7860 (p90) REVERT: B 688 MET cc_start: 0.8840 (mmp) cc_final: 0.8510 (mmm) REVERT: C 49 TRP cc_start: 0.8893 (t-100) cc_final: 0.7818 (t60) REVERT: C 50 MET cc_start: 0.8388 (ptm) cc_final: 0.7900 (tpp) REVERT: C 51 MET cc_start: 0.8697 (tpp) cc_final: 0.8376 (tpp) REVERT: C 90 MET cc_start: 0.5131 (mtm) cc_final: 0.4601 (ptm) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.2644 time to fit residues: 102.1441 Evaluate side-chains 228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 292 ASN B 313 GLN B 328 ASN B 413 ASN B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS C 170 ASN F 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.112150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.093209 restraints weight = 209431.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.097466 restraints weight = 110356.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.100207 restraints weight = 66069.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.102046 restraints weight = 44088.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.103077 restraints weight = 32178.756| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 15299 Z= 0.295 Angle : 0.808 28.367 20738 Z= 0.436 Chirality : 0.042 0.178 2276 Planarity : 0.007 0.111 2590 Dihedral : 7.705 74.836 2235 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % 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: -1.74 (0.18), residues: 1781 helix: -0.64 (0.16), residues: 806 sheet: -0.72 (0.36), residues: 206 loop : -1.76 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 116 TYR 0.028 0.003 TYR B 30 PHE 0.043 0.003 PHE A 411 TRP 0.038 0.003 TRP B 613 HIS 0.016 0.003 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.29 (15298) covalent geometry : angle 0.80812 / 0.44 (20736) SS BOND : bond 0.00902 / 0.43 ( 1) SS BOND : angle 2.10370 / 1.20 ( 2) hydrogen bonds : bond 0.05083 / 3.33 ( 732) hydrogen bonds : angle 5.63349 / 4.03 ( 2006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 253 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 0.648 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: A 12 MET cc_start: 0.0679 (ppp) cc_final: 0.0141 (ppp) REVERT: A 334 TYR cc_start: 0.8560 (m-80) cc_final: 0.7811 (m-10) REVERT: A 389 ASP cc_start: 0.5940 (t0) cc_final: 0.5471 (t70) REVERT: A 477 MET cc_start: 0.6905 (mtp) cc_final: 0.5346 (ttp) REVERT: A 543 LEU cc_start: 0.9367 (mt) cc_final: 0.8953 (tp) REVERT: A 581 MET cc_start: 0.8416 (mtp) cc_final: 0.7485 (mtp) REVERT: A 585 LEU cc_start: 0.8035 (mt) cc_final: 0.7045 (tp) REVERT: B 40 MET cc_start: 0.9020 (mtp) cc_final: 0.8055 (ttm) REVERT: B 317 MET cc_start: 0.9178 (ttm) cc_final: 0.8939 (ttt) REVERT: B 411 MET cc_start: 0.8642 (mmm) cc_final: 0.7658 (mmm) REVERT: B 414 MET cc_start: 0.3797 (mmm) cc_final: 0.3482 (mmt) REVERT: B 425 ASN cc_start: 0.9299 (t160) cc_final: 0.8981 (t0) REVERT: B 645 MET cc_start: 0.7905 (mpp) cc_final: 0.7292 (mpp) REVERT: B 657 TYR cc_start: 0.8406 (p90) cc_final: 0.8085 (p90) REVERT: B 718 MET cc_start: 0.8921 (mtp) cc_final: 0.8353 (mmm) REVERT: C 67 ILE cc_start: 0.8046 (mt) cc_final: 0.7803 (tt) outliers start: 2 outliers final: 1 residues processed: 253 average time/residue: 0.2574 time to fit residues: 96.1083 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 537 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.115125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.095884 restraints weight = 201304.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.100313 restraints weight = 104621.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.103220 restraints weight = 62049.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.105124 restraints weight = 40794.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.106410 restraints weight = 29457.294| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15299 Z= 0.132 Angle : 0.582 25.322 20738 Z= 0.307 Chirality : 0.038 0.188 2276 Planarity : 0.005 0.117 2590 Dihedral : 7.218 76.132 2235 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 1781 helix: 0.18 (0.17), residues: 794 sheet: -0.71 (0.36), residues: 206 loop : -1.46 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 124 TYR 0.016 0.001 TYR B 497 PHE 0.035 0.002 PHE B 501 TRP 0.008 0.001 TRP C 240 HIS 0.024 0.002 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15298) covalent geometry : angle 0.58212 / 0.31 (20736) SS BOND : bond 0.00277 / 0.13 ( 1) SS BOND : angle 0.62752 / 0.36 ( 2) hydrogen bonds : bond 0.04015 / 2.65 ( 732) hydrogen bonds : angle 4.94921 / 3.53 ( 2006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 245 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.729 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 260 PHE cc_start: 0.6380 (t80) cc_final: 0.5685 (t80) REVERT: A 334 TYR cc_start: 0.8524 (m-80) cc_final: 0.7655 (m-10) REVERT: A 389 ASP cc_start: 0.4905 (t0) cc_final: 0.4425 (t70) REVERT: A 459 ILE cc_start: 0.7646 (mt) cc_final: 0.6482 (mt) REVERT: A 513 ASN cc_start: 0.8632 (m-40) cc_final: 0.8431 (m-40) REVERT: A 525 PHE cc_start: 0.7732 (m-80) cc_final: 0.6574 (m-80) REVERT: A 543 LEU cc_start: 0.9317 (mt) cc_final: 0.8961 (mt) REVERT: A 581 MET cc_start: 0.8066 (mtp) cc_final: 0.6782 (mtp) REVERT: A 585 LEU cc_start: 0.8376 (mt) cc_final: 0.7450 (tp) REVERT: A 672 LEU cc_start: 0.7050 (tp) cc_final: 0.6722 (tp) REVERT: B 24 TYR cc_start: 0.8171 (m-80) cc_final: 0.7916 (m-80) REVERT: B 40 MET cc_start: 0.8850 (mtp) cc_final: 0.8046 (ttp) REVERT: B 127 GLN cc_start: 0.6727 (mm-40) cc_final: 0.6283 (mm110) REVERT: B 224 LEU cc_start: 0.7822 (mt) cc_final: 0.7542 (mt) REVERT: B 317 MET cc_start: 0.9048 (tpp) cc_final: 0.8613 (tpp) REVERT: B 347 LYS cc_start: 0.8809 (pttm) cc_final: 0.8075 (pttm) REVERT: B 348 MET cc_start: 0.6491 (mmp) cc_final: 0.5666 (mmt) REVERT: B 356 MET cc_start: 0.8955 (ttm) cc_final: 0.8594 (ttm) REVERT: B 411 MET cc_start: 0.8365 (mmm) cc_final: 0.7278 (mmm) REVERT: B 425 ASN cc_start: 0.9255 (t160) cc_final: 0.8846 (t0) REVERT: B 522 ASP cc_start: 0.7727 (m-30) cc_final: 0.7279 (t70) REVERT: B 532 ASN cc_start: 0.8746 (m-40) cc_final: 0.8535 (m-40) REVERT: B 645 MET cc_start: 0.8131 (mpp) cc_final: 0.7318 (mpp) REVERT: B 657 TYR cc_start: 0.8737 (p90) cc_final: 0.8371 (p90) REVERT: B 718 MET cc_start: 0.8898 (mtp) cc_final: 0.8277 (mmm) REVERT: C 50 MET cc_start: 0.8946 (tpp) cc_final: 0.8515 (tpp) REVERT: C 53 MET cc_start: 0.6957 (ttt) cc_final: 0.6611 (ttm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2515 time to fit residues: 91.8041 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 10 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 582 GLN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.113515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.094395 restraints weight = 203715.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098800 restraints weight = 105478.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.101689 restraints weight = 62457.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.103543 restraints weight = 41027.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.104848 restraints weight = 29640.194| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15299 Z= 0.140 Angle : 0.568 27.335 20738 Z= 0.300 Chirality : 0.038 0.177 2276 Planarity : 0.005 0.065 2590 Dihedral : 7.062 78.122 2235 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.79 (0.19), residues: 1781 helix: 0.40 (0.18), residues: 803 sheet: -0.76 (0.36), residues: 206 loop : -1.41 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 233 TYR 0.027 0.002 TYR B 82 PHE 0.026 0.002 PHE B 631 TRP 0.011 0.001 TRP B 613 HIS 0.008 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (15298) covalent geometry : angle 0.56819 / 0.30 (20736) SS BOND : bond 0.00334 / 0.16 ( 1) SS BOND : angle 0.68000 / 0.40 ( 2) hydrogen bonds : bond 0.03806 / 2.53 ( 732) hydrogen bonds : angle 4.87873 / 3.47 ( 2006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 244 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 PHE cc_start: 0.6482 (t80) cc_final: 0.5745 (t80) REVERT: A 334 TYR cc_start: 0.8533 (m-80) cc_final: 0.7690 (m-10) REVERT: A 389 ASP cc_start: 0.5122 (t0) cc_final: 0.4545 (t70) REVERT: A 459 ILE cc_start: 0.7750 (mt) cc_final: 0.6522 (mt) REVERT: A 477 MET cc_start: 0.6802 (mtp) cc_final: 0.5837 (ptt) REVERT: A 513 ASN cc_start: 0.8515 (m-40) cc_final: 0.8288 (m-40) REVERT: A 543 LEU cc_start: 0.9341 (mt) cc_final: 0.8977 (mt) REVERT: A 581 MET cc_start: 0.8163 (mtp) cc_final: 0.6824 (mtp) REVERT: A 585 LEU cc_start: 0.8244 (mt) cc_final: 0.7096 (tp) REVERT: A 672 LEU cc_start: 0.7000 (tp) cc_final: 0.6498 (tp) REVERT: B 40 MET cc_start: 0.8946 (mtp) cc_final: 0.8156 (ttp) REVERT: B 127 GLN cc_start: 0.5160 (mm-40) cc_final: 0.4950 (mm110) REVERT: B 348 MET cc_start: 0.6532 (mmp) cc_final: 0.5772 (mmt) REVERT: B 407 MET cc_start: 0.8935 (tpp) cc_final: 0.8616 (tpp) REVERT: B 411 MET cc_start: 0.8422 (mmm) cc_final: 0.7215 (mmm) REVERT: B 425 ASN cc_start: 0.9282 (t160) cc_final: 0.8973 (t0) REVERT: B 522 ASP cc_start: 0.7754 (m-30) cc_final: 0.7538 (t70) REVERT: B 645 MET cc_start: 0.8149 (mpp) cc_final: 0.7270 (mpp) REVERT: B 657 TYR cc_start: 0.8661 (p90) cc_final: 0.8382 (p90) REVERT: B 692 CYS cc_start: 0.8350 (m) cc_final: 0.7944 (p) REVERT: B 718 MET cc_start: 0.8932 (mtp) cc_final: 0.8236 (mmm) REVERT: C 50 MET cc_start: 0.8914 (tpp) cc_final: 0.8692 (tpp) REVERT: C 53 MET cc_start: 0.6889 (ttt) cc_final: 0.6554 (ttm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2419 time to fit residues: 88.2026 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 425 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.110195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.091155 restraints weight = 209291.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.095371 restraints weight = 108917.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.098102 restraints weight = 65038.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099932 restraints weight = 43439.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.101120 restraints weight = 31783.843| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15299 Z= 0.176 Angle : 0.603 26.216 20738 Z= 0.321 Chirality : 0.038 0.156 2276 Planarity : 0.005 0.090 2590 Dihedral : 7.217 82.491 2235 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 1781 helix: 0.33 (0.18), residues: 789 sheet: -0.86 (0.36), residues: 207 loop : -1.44 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 88 TYR 0.019 0.002 TYR F 95 PHE 0.019 0.002 PHE B 730 TRP 0.018 0.002 TRP C 240 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (15298) covalent geometry : angle 0.60344 / 0.32 (20736) SS BOND : bond 0.00570 / 0.27 ( 1) SS BOND : angle 0.62088 / 0.36 ( 2) hydrogen bonds : bond 0.03970 / 2.65 ( 732) hydrogen bonds : angle 5.00059 / 3.55 ( 2006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.789 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: A 211 MET cc_start: 0.7803 (mpp) cc_final: 0.7544 (mtm) REVERT: A 260 PHE cc_start: 0.6537 (t80) cc_final: 0.5859 (t80) REVERT: A 334 TYR cc_start: 0.8515 (m-80) cc_final: 0.7550 (m-10) REVERT: A 389 ASP cc_start: 0.5478 (t0) cc_final: 0.4905 (t0) REVERT: A 436 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6323 (mt-10) REVERT: A 459 ILE cc_start: 0.7911 (mt) cc_final: 0.7617 (mt) REVERT: A 477 MET cc_start: 0.6861 (mtp) cc_final: 0.5694 (ptt) REVERT: A 525 PHE cc_start: 0.8075 (m-80) cc_final: 0.6705 (m-80) REVERT: A 543 LEU cc_start: 0.9360 (mt) cc_final: 0.9003 (mt) REVERT: A 563 LEU cc_start: 0.7337 (tp) cc_final: 0.6917 (tp) REVERT: A 579 MET cc_start: 0.8238 (ttt) cc_final: 0.7609 (ttt) REVERT: A 581 MET cc_start: 0.8281 (mtp) cc_final: 0.6858 (mtp) REVERT: A 589 LEU cc_start: 0.8480 (mm) cc_final: 0.7900 (mt) REVERT: A 672 LEU cc_start: 0.6722 (tp) cc_final: 0.6072 (tp) REVERT: B 40 MET cc_start: 0.9037 (mtp) cc_final: 0.8223 (ttp) REVERT: B 224 LEU cc_start: 0.7622 (mt) cc_final: 0.7306 (mp) REVERT: B 347 LYS cc_start: 0.8561 (pttm) cc_final: 0.7960 (pttm) REVERT: B 407 MET cc_start: 0.8961 (tpp) cc_final: 0.8668 (tpp) REVERT: B 411 MET cc_start: 0.8554 (mmm) cc_final: 0.7320 (mmm) REVERT: B 414 MET cc_start: 0.3708 (mmm) cc_final: 0.3187 (mmt) REVERT: B 425 ASN cc_start: 0.9365 (t160) cc_final: 0.8971 (t0) REVERT: B 532 ASN cc_start: 0.8721 (m-40) cc_final: 0.8517 (m-40) REVERT: B 645 MET cc_start: 0.8195 (mpp) cc_final: 0.7103 (mpp) REVERT: B 657 TYR cc_start: 0.8659 (p90) cc_final: 0.8456 (p90) REVERT: B 688 MET cc_start: 0.8962 (mmp) cc_final: 0.8713 (mmp) REVERT: B 692 CYS cc_start: 0.8455 (m) cc_final: 0.8021 (p) REVERT: B 718 MET cc_start: 0.8941 (mtp) cc_final: 0.8323 (mmm) REVERT: C 49 TRP cc_start: 0.9366 (t-100) cc_final: 0.8539 (t60) REVERT: C 53 MET cc_start: 0.7002 (ttt) cc_final: 0.6575 (ttm) REVERT: F 34 MET cc_start: 0.5190 (tpt) cc_final: 0.4963 (tpt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2551 time to fit residues: 87.6172 Evaluate side-chains 208 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 425 ASN B 634 HIS ** C 73 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 = 0.4204 r_free = 0.4204 target = 0.111411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092406 restraints weight = 203637.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.096746 restraints weight = 104368.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.099562 restraints weight = 61855.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.101401 restraints weight = 40854.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.102442 restraints weight = 29836.601| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15299 Z= 0.113 Angle : 0.544 26.600 20738 Z= 0.284 Chirality : 0.038 0.152 2276 Planarity : 0.005 0.114 2590 Dihedral : 7.014 83.977 2235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1781 helix: 0.61 (0.18), residues: 799 sheet: -0.78 (0.36), residues: 207 loop : -1.33 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 88 TYR 0.014 0.001 TYR B 30 PHE 0.016 0.001 PHE B 730 TRP 0.019 0.001 TRP C 49 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15298) covalent geometry : angle 0.54382 / 0.28 (20736) SS BOND : bond 0.00276 / 0.13 ( 1) SS BOND : angle 0.37059 / 0.21 ( 2) hydrogen bonds : bond 0.03660 / 2.43 ( 732) hydrogen bonds : angle 4.69726 / 3.32 ( 2006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 236 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8527 (m-80) cc_final: 0.7566 (m-10) REVERT: A 389 ASP cc_start: 0.5497 (t0) cc_final: 0.5019 (t0) REVERT: A 459 ILE cc_start: 0.7686 (mt) cc_final: 0.7418 (mt) REVERT: A 477 MET cc_start: 0.6493 (mtp) cc_final: 0.5489 (ptt) REVERT: A 543 LEU cc_start: 0.9339 (mt) cc_final: 0.8973 (mt) REVERT: A 581 MET cc_start: 0.8251 (mtp) cc_final: 0.6792 (mtp) REVERT: B 40 MET cc_start: 0.9035 (mtp) cc_final: 0.8202 (ttp) REVERT: B 348 MET cc_start: 0.6650 (mmp) cc_final: 0.6062 (mmt) REVERT: B 407 MET cc_start: 0.8986 (tpp) cc_final: 0.8534 (tpp) REVERT: B 411 MET cc_start: 0.8502 (mmm) cc_final: 0.7322 (mmm) REVERT: B 414 MET cc_start: 0.3563 (mmm) cc_final: 0.3084 (mmt) REVERT: B 425 ASN cc_start: 0.9379 (t160) cc_final: 0.9058 (t0) REVERT: B 645 MET cc_start: 0.8157 (mpp) cc_final: 0.7111 (mpp) REVERT: B 657 TYR cc_start: 0.8698 (p90) cc_final: 0.8492 (p90) REVERT: B 688 MET cc_start: 0.8948 (mmp) cc_final: 0.7944 (mtt) REVERT: B 692 CYS cc_start: 0.8462 (m) cc_final: 0.8008 (p) REVERT: B 718 MET cc_start: 0.8949 (mtp) cc_final: 0.8354 (mmm) REVERT: C 50 MET cc_start: 0.9050 (tpp) cc_final: 0.8705 (tpp) REVERT: C 53 MET cc_start: 0.6955 (ttt) cc_final: 0.6571 (ttm) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2795 time to fit residues: 98.4191 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 466 ASN B 425 ASN B 634 HIS ** C 73 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 = 0.4169 r_free = 0.4169 target = 0.108885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.090012 restraints weight = 208089.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.094205 restraints weight = 107692.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.096911 restraints weight = 64193.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.098754 restraints weight = 42934.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.099961 restraints weight = 31369.865| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15299 Z= 0.152 Angle : 0.576 26.047 20738 Z= 0.305 Chirality : 0.038 0.152 2276 Planarity : 0.005 0.069 2590 Dihedral : 7.039 86.493 2235 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1781 helix: 0.53 (0.18), residues: 798 sheet: -0.82 (0.36), residues: 206 loop : -1.31 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 663 TYR 0.016 0.002 TYR B 30 PHE 0.017 0.002 PHE B 730 TRP 0.014 0.002 TRP B 613 HIS 0.005 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (15298) covalent geometry : angle 0.57553 / 0.31 (20736) SS BOND : bond 0.00475 / 0.23 ( 1) SS BOND : angle 0.68811 / 0.39 ( 2) hydrogen bonds : bond 0.03750 / 2.48 ( 732) hydrogen bonds : angle 4.82762 / 3.43 ( 2006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 233 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.590 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: A 211 MET cc_start: 0.7871 (mpp) cc_final: 0.7308 (mtm) REVERT: A 214 LEU cc_start: 0.8526 (mt) cc_final: 0.8210 (mt) REVERT: A 260 PHE cc_start: 0.6615 (t80) cc_final: 0.5979 (t80) REVERT: A 389 ASP cc_start: 0.5887 (t0) cc_final: 0.5280 (t0) REVERT: A 459 ILE cc_start: 0.7879 (mt) cc_final: 0.7594 (mt) REVERT: A 477 MET cc_start: 0.7283 (mtp) cc_final: 0.6158 (ptt) REVERT: A 525 PHE cc_start: 0.8042 (m-80) cc_final: 0.6426 (m-80) REVERT: A 543 LEU cc_start: 0.9373 (mt) cc_final: 0.9019 (mt) REVERT: A 563 LEU cc_start: 0.7527 (tp) cc_final: 0.7280 (tp) REVERT: A 581 MET cc_start: 0.8904 (mtp) cc_final: 0.7649 (mtp) REVERT: A 672 LEU cc_start: 0.6902 (tp) cc_final: 0.6521 (tp) REVERT: B 40 MET cc_start: 0.9081 (mtp) cc_final: 0.8262 (ttp) REVERT: B 224 LEU cc_start: 0.7765 (mt) cc_final: 0.7398 (mt) REVERT: B 262 ILE cc_start: 0.4800 (mm) cc_final: 0.4587 (mm) REVERT: B 347 LYS cc_start: 0.8487 (pttm) cc_final: 0.7909 (pttm) REVERT: B 407 MET cc_start: 0.9098 (tpp) cc_final: 0.8682 (tpp) REVERT: B 411 MET cc_start: 0.8602 (mmm) cc_final: 0.7493 (mmm) REVERT: B 414 MET cc_start: 0.3676 (mmm) cc_final: 0.3088 (mmt) REVERT: B 425 ASN cc_start: 0.9402 (t160) cc_final: 0.8982 (t0) REVERT: B 645 MET cc_start: 0.8179 (mpp) cc_final: 0.7142 (mpp) REVERT: B 688 MET cc_start: 0.9089 (mmp) cc_final: 0.7974 (mtt) REVERT: B 692 CYS cc_start: 0.8530 (m) cc_final: 0.8075 (p) REVERT: B 718 MET cc_start: 0.8913 (mtp) cc_final: 0.8323 (mmm) REVERT: C 49 TRP cc_start: 0.9339 (t-100) cc_final: 0.8560 (t60) REVERT: C 53 MET cc_start: 0.6982 (ttt) cc_final: 0.6596 (ttm) REVERT: C 170 ASN cc_start: 0.8208 (m-40) cc_final: 0.7912 (m-40) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2559 time to fit residues: 89.5628 Evaluate side-chains 206 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 50 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 634 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.107680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.088903 restraints weight = 208126.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.093016 restraints weight = 107686.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.095729 restraints weight = 64554.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.097529 restraints weight = 43295.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.098744 restraints weight = 31767.826| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15299 Z= 0.147 Angle : 0.564 26.473 20738 Z= 0.300 Chirality : 0.038 0.153 2276 Planarity : 0.005 0.068 2590 Dihedral : 7.087 88.408 2235 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1781 helix: 0.56 (0.18), residues: 792 sheet: -0.82 (0.36), residues: 207 loop : -1.36 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 443 TYR 0.012 0.002 TYR B 82 PHE 0.016 0.002 PHE B 730 TRP 0.013 0.002 TRP C 49 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (15298) covalent geometry : angle 0.56447 / 0.30 (20736) SS BOND : bond 0.00348 / 0.17 ( 1) SS BOND : angle 0.49532 / 0.28 ( 2) hydrogen bonds : bond 0.03713 / 2.45 ( 732) hydrogen bonds : angle 4.86615 / 3.45 ( 2006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 226 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.809 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: A 214 LEU cc_start: 0.8532 (mt) cc_final: 0.8262 (mt) REVERT: A 257 ILE cc_start: 0.7747 (tt) cc_final: 0.7485 (tp) REVERT: A 260 PHE cc_start: 0.6665 (t80) cc_final: 0.6015 (t80) REVERT: A 389 ASP cc_start: 0.5674 (t0) cc_final: 0.5184 (t0) REVERT: A 436 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6041 (tt0) REVERT: A 459 ILE cc_start: 0.7878 (mt) cc_final: 0.7609 (mt) REVERT: A 477 MET cc_start: 0.7411 (mtp) cc_final: 0.6188 (ptt) REVERT: A 575 MET cc_start: 0.8420 (tpp) cc_final: 0.8110 (tpp) REVERT: A 581 MET cc_start: 0.8948 (mtp) cc_final: 0.7686 (mtp) REVERT: A 672 LEU cc_start: 0.7004 (tp) cc_final: 0.6626 (tp) REVERT: B 40 MET cc_start: 0.9093 (mtp) cc_final: 0.8305 (ttp) REVERT: B 407 MET cc_start: 0.9170 (tpp) cc_final: 0.8653 (tpp) REVERT: B 411 MET cc_start: 0.8597 (mmm) cc_final: 0.7560 (mmm) REVERT: B 414 MET cc_start: 0.3610 (mmm) cc_final: 0.3024 (mmt) REVERT: B 425 ASN cc_start: 0.9363 (t160) cc_final: 0.9106 (t0) REVERT: B 483 TYR cc_start: 0.8030 (p90) cc_final: 0.7571 (p90) REVERT: B 532 ASN cc_start: 0.8668 (m-40) cc_final: 0.8398 (m-40) REVERT: B 645 MET cc_start: 0.8201 (mpp) cc_final: 0.7119 (mpp) REVERT: B 657 TYR cc_start: 0.8163 (p90) cc_final: 0.7577 (p90) REVERT: B 688 MET cc_start: 0.9116 (mmp) cc_final: 0.8012 (mtt) REVERT: B 692 CYS cc_start: 0.8543 (m) cc_final: 0.8201 (p) REVERT: B 718 MET cc_start: 0.9021 (mtp) cc_final: 0.8524 (mmm) REVERT: C 50 MET cc_start: 0.8971 (tpp) cc_final: 0.8653 (tpp) REVERT: C 53 MET cc_start: 0.7088 (ttt) cc_final: 0.6707 (ttm) REVERT: C 170 ASN cc_start: 0.8258 (m-40) cc_final: 0.7966 (m-40) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2749 time to fit residues: 93.2502 Evaluate side-chains 202 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN B 425 ASN B 569 GLN B 634 HIS ** C 73 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 = 0.4148 r_free = 0.4148 target = 0.107343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.088447 restraints weight = 211681.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092563 restraints weight = 109515.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.095273 restraints weight = 65650.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.097070 restraints weight = 44064.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.098295 restraints weight = 32531.964| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.7623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15299 Z= 0.125 Angle : 0.547 26.258 20738 Z= 0.287 Chirality : 0.038 0.152 2276 Planarity : 0.004 0.060 2590 Dihedral : 7.005 89.215 2235 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1781 helix: 0.68 (0.18), residues: 792 sheet: -0.79 (0.36), residues: 197 loop : -1.32 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 443 TYR 0.015 0.001 TYR B 24 PHE 0.016 0.001 PHE B 730 TRP 0.010 0.001 TRP C 49 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15298) covalent geometry : angle 0.54729 / 0.29 (20736) SS BOND : bond 0.00344 / 0.16 ( 1) SS BOND : angle 0.60315 / 0.35 ( 2) hydrogen bonds : bond 0.03575 / 2.35 ( 732) hydrogen bonds : angle 4.81422 / 3.41 ( 2006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4537.33 seconds wall clock time: 78 minutes 26.58 seconds (4706.58 seconds total)