Starting phenix.real_space_refine on Wed Aug 5 20:34:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.map" model { file = "/net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycm_72777/08_2026/9ycm_72777.cif" } resolution = 2.94 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= 0.001 sd= 0.024 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 64 5.49 5 Mg 2 5.21 5 S 88 5.16 5 C 6976 2.51 5 N 1952 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11376 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 971 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 971 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "B" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4009 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 702 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain breaks: 1 Chain: "E" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4009 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 476} Chain breaks: 1 Chain: "F" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 702 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 74 36.529 37.078 36.938 1.00 74.23 S ATOM 553 SG CYS A 77 34.368 38.234 39.969 1.00 76.68 S ATOM 651 SG CYS A 90 33.629 39.604 36.440 1.00 83.66 S ATOM 859 SG CYS A 117 32.396 36.410 16.800 1.00159.96 S ATOM 880 SG CYS A 120 29.287 34.182 16.649 1.00153.09 S ATOM 949 SG CYS A 128 32.634 32.665 16.041 1.00155.85 S ATOM 963 SG CYS A 130 31.196 34.908 13.423 1.00176.98 S ATOM 1498 SG CYS D 74 90.676 77.039 36.937 1.00 72.08 S ATOM 1524 SG CYS D 77 92.898 75.892 39.912 1.00 73.50 S ATOM 1622 SG CYS D 90 93.560 74.519 36.388 1.00 83.62 S ATOM 1830 SG CYS D 117 94.867 77.711 16.794 1.00156.63 S ATOM 1851 SG CYS D 120 97.928 79.975 16.648 1.00150.81 S ATOM 1920 SG CYS D 128 94.560 81.436 16.011 1.00153.42 S ATOM 1934 SG CYS D 130 96.051 79.204 13.400 1.00172.86 S ATOM 3547 SG CYS B 207 67.902 46.077 37.277 1.00 85.73 S ATOM 3567 SG CYS B 210 71.676 45.468 37.686 1.00 89.75 S ATOM 3689 SG CYS B 226 69.538 46.218 40.703 1.00 91.64 S ATOM 3988 SG CYS B 261 68.745 41.624 73.500 1.00101.62 S ATOM 4118 SG CYS B 279 68.385 39.579 70.137 1.00 95.59 S ATOM 5493 SG CYS B 448 118.646 46.339 56.396 1.00181.04 S ATOM 5576 SG CYS B 474 118.293 49.984 57.218 1.00168.07 S ATOM 5618 SG CYS B 481 116.255 48.568 54.301 1.00177.26 S ATOM 8258 SG CYS E 207 59.280 68.023 37.239 1.00 86.36 S ATOM 8278 SG CYS E 210 55.523 68.692 37.700 1.00 90.89 S ATOM 8400 SG CYS E 226 57.688 67.893 40.683 1.00 89.91 S ATOM 8699 SG CYS E 261 58.454 72.533 73.530 1.00104.67 S ATOM 8829 SG CYS E 279 58.831 74.534 70.140 1.00 97.79 S ATOM 10204 SG CYS E 448 8.613 67.751 56.229 1.00179.52 S ATOM 10287 SG CYS E 474 8.901 64.172 57.296 1.00172.79 S ATOM 10329 SG CYS E 481 10.929 65.342 54.282 1.00175.13 S Time building chain proxies: 2.78, per 1000 atoms: 0.24 Number of scatterers: 11376 At special positions: 0 Unit cell: (128.136, 114.107, 95.4006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 88 16.00 P 64 15.00 Mg 2 11.99 O 2284 8.00 N 1952 7.00 C 6976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.99 Conformation dependent library (CDL) restraints added in 513.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 474 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 448 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 481 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 90 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 77 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 74 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 128 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 120 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 130 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 117 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" ND1 HIS E 229 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 226 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 210 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 207 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 257 " pdb="ZN ZN E 603 " - pdb=" ND1 HIS E 264 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 261 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 279 " pdb=" ZN E 604 " pdb="ZN ZN E 604 " - pdb=" ND1 HIS E 484 " pdb="ZN ZN E 604 " - pdb=" SG CYS E 474 " pdb="ZN ZN E 604 " - pdb=" SG CYS E 448 " pdb="ZN ZN E 604 " - pdb=" SG CYS E 481 " Number of angles added : 33 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 18 sheets defined 31.4% alpha, 17.6% beta 26 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 22 through 33 Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.844A pdb=" N GLU B 38 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 146 through 155 Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.524A pdb=" N ARG B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.806A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.693A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 301 through 324 removed outlier: 3.805A pdb=" N GLY B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 4.404A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 374 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.651A pdb=" N LEU B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 477' Processing helix chain 'B' and resid 481 through 502 Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.665A pdb=" N TRP B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 518 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 82 Processing helix chain 'E' and resid 146 through 155 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 158 through 175 removed outlier: 3.651A pdb=" N ARG E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 removed outlier: 3.806A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 248 removed outlier: 3.678A pdb=" N GLY E 248 " --> pdb=" O GLN E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 252 through 259 removed outlier: 3.562A pdb=" N ARG E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 301 through 323 Processing helix chain 'E' and resid 366 through 374 removed outlier: 4.465A pdb=" N SER E 371 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 374 " --> pdb=" O SER E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 removed outlier: 3.537A pdb=" N ARG E 433 " --> pdb=" O SER E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 477 removed outlier: 3.585A pdb=" N LEU E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 472 through 477' Processing helix chain 'E' and resid 481 through 502 Processing helix chain 'E' and resid 512 through 519 removed outlier: 3.586A pdb=" N TRP E 517 " --> pdb=" O TYR E 514 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 518 " --> pdb=" O ASN E 515 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR E 519 " --> pdb=" O LEU E 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 4.513A pdb=" N GLU A 6 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.537A pdb=" N GLU D 6 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 55 removed outlier: 4.241A pdb=" N VAL B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.083A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.083A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362 removed outlier: 5.076A pdb=" N TRP B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B 392 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AB2, first strand: chain 'B' and resid 442 through 443 removed outlier: 6.606A pdb=" N TYR B 442 " --> pdb=" O ILE B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 52 through 55 removed outlier: 4.238A pdb=" N VAL E 124 " --> pdb=" O ILE E 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 116 through 118 removed outlier: 7.035A pdb=" N ASN E 104 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 96 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA E 94 " --> pdb=" O PRO E 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 118 removed outlier: 7.035A pdb=" N ASN E 104 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 96 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA E 94 " --> pdb=" O PRO E 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AB7, first strand: chain 'E' and resid 361 through 362 removed outlier: 3.620A pdb=" N GLN E 361 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP E 381 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA E 392 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 406 through 408 Processing sheet with id=AB9, first strand: chain 'E' and resid 442 through 443 removed outlier: 6.527A pdb=" N TYR E 442 " --> pdb=" O ILE E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 364 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3344 1.34 - 1.46: 2690 1.46 - 1.58: 5544 1.58 - 1.69: 126 1.69 - 1.81: 106 Bond restraints: 11810 Sorted by residual: bond pdb=" N PHE E 405 " pdb=" CA PHE E 405 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.55e+00 bond pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 6.86e+00 bond pdb=" N ASN E 99 " pdb=" CA ASN E 99 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.35e-02 5.49e+03 6.25e+00 bond pdb=" N LYS E 336 " pdb=" CA LYS E 336 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.10e+00 bond pdb=" N CYS E 378 " pdb=" CA CYS E 378 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.27e-02 6.20e+03 5.96e+00 ... (remaining 11805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15840 1.74 - 3.47: 496 3.47 - 5.21: 36 5.21 - 6.95: 8 6.95 - 8.68: 2 Bond angle restraints: 16382 Sorted by residual: angle pdb=" O5' G F 9 " pdb=" C5' G F 9 " pdb=" C4' G F 9 " ideal model delta sigma weight residual 109.40 112.68 -3.28 8.00e-01 1.56e+00 1.68e+01 angle pdb=" O5' G C 9 " pdb=" C5' G C 9 " pdb=" C4' G C 9 " ideal model delta sigma weight residual 109.40 112.62 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" O5' A C 32 " pdb=" C5' A C 32 " pdb=" C4' A C 32 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' G C 1 " pdb=" C5' G C 1 " pdb=" C4' G C 1 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.15e+01 angle pdb=" O5' G F 1 " pdb=" C5' G F 1 " pdb=" C4' G F 1 " ideal model delta sigma weight residual 109.40 112.09 -2.69 8.00e-01 1.56e+00 1.13e+01 ... (remaining 16377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.69: 6420 18.69 - 37.38: 394 37.38 - 56.07: 80 56.07 - 74.77: 75 74.77 - 93.46: 9 Dihedral angle restraints: 6978 sinusoidal: 3266 harmonic: 3712 Sorted by residual: dihedral pdb=" O4' A C 4 " pdb=" C1' A C 4 " pdb=" N9 A C 4 " pdb=" C4 A C 4 " ideal model delta sinusoidal sigma weight residual 70.00 1.50 68.50 1 2.00e+01 2.50e-03 1.52e+01 dihedral pdb=" O4' A F 4 " pdb=" C1' A F 4 " pdb=" N9 A F 4 " pdb=" C4 A F 4 " ideal model delta sinusoidal sigma weight residual 70.00 2.63 67.37 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" CG ARG B 163 " pdb=" CD ARG B 163 " pdb=" NE ARG B 163 " pdb=" CZ ARG B 163 " ideal model delta sinusoidal sigma weight residual 180.00 135.56 44.44 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1251 0.040 - 0.079: 372 0.079 - 0.119: 122 0.119 - 0.158: 87 0.158 - 0.198: 2 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C1' G C 2 " pdb=" O4' G C 2 " pdb=" C2' G C 2 " pdb=" N9 G C 2 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" C1' G F 2 " pdb=" O4' G F 2 " pdb=" C2' G F 2 " pdb=" N9 G F 2 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1831 not shown) Planarity restraints: 1866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 213 " 0.193 9.50e-02 1.11e+02 8.64e-02 4.59e+00 pdb=" NE ARG B 213 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 213 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 213 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 213 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 19 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO E 20 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 20 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 20 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G F 2 " -0.023 2.00e-02 2.50e+03 1.04e-02 3.25e+00 pdb=" N9 G F 2 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G F 2 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G F 2 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G F 2 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G F 2 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G F 2 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G F 2 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G F 2 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G F 2 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G F 2 " 0.000 2.00e-02 2.50e+03 ... (remaining 1863 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 36 2.64 - 3.20: 9590 3.20 - 3.77: 17962 3.77 - 4.33: 25436 4.33 - 4.90: 40053 Nonbonded interactions: 93077 Sorted by model distance: nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.071 2.170 nonbonded pdb=" OD2 ASP E 90 " pdb="MG MG E 601 " model vdw 2.071 2.170 nonbonded pdb=" OP1 U C 39 " pdb="MG MG B 601 " model vdw 2.089 2.170 nonbonded pdb=" OP1 U F 39 " pdb="MG MG E 601 " model vdw 2.089 2.170 nonbonded pdb=" OE2 GLU E 92 " pdb="MG MG E 601 " model vdw 2.093 2.170 ... (remaining 93072 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.680 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.003 0.037 11850 Z= 0.188 Angle : 0.665 8.684 16415 Z= 0.445 Chirality : 0.049 0.198 1834 Planarity : 0.005 0.086 1866 Dihedral : 14.580 93.457 4602 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.33 (0.23), residues: 1260 helix: -0.07 (0.28), residues: 318 sheet: -0.74 (0.43), residues: 144 loop : -0.08 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 433 TYR 0.011 0.001 TYR B 491 PHE 0.010 0.001 PHE D 30 TRP 0.011 0.001 TRP B 381 HIS 0.007 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.19 (11810) covalent geometry : angle 0.65834 / 0.44 (16382) hydrogen bonds : bond 0.15139 / 10.40 ( 412) hydrogen bonds : angle 5.41147 / 3.93 ( 1077) metal coordination : bond 0.00909 / 0.57 ( 40) metal coordination : angle 2.14820 / 1.51 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7564 (t) cc_final: 0.7281 (m) REVERT: A 114 ASN cc_start: 0.7805 (m110) cc_final: 0.7464 (m110) REVERT: D 89 VAL cc_start: 0.7804 (t) cc_final: 0.7486 (m) REVERT: B 38 GLU cc_start: 0.6759 (tt0) cc_final: 0.6541 (tt0) REVERT: B 51 TYR cc_start: 0.8157 (p90) cc_final: 0.7875 (p90) REVERT: B 78 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7295 (mt-10) REVERT: B 92 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7195 (mp0) REVERT: B 97 SER cc_start: 0.8061 (p) cc_final: 0.7772 (m) REVERT: B 126 ASP cc_start: 0.7618 (t70) cc_final: 0.7288 (m-30) REVERT: B 164 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7779 (mtt90) REVERT: B 172 ASP cc_start: 0.7477 (m-30) cc_final: 0.7088 (m-30) REVERT: B 276 MET cc_start: 0.7848 (mtm) cc_final: 0.7641 (mtp) REVERT: B 295 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 304 LYS cc_start: 0.7020 (tttp) cc_final: 0.6726 (tttm) REVERT: B 328 LYS cc_start: 0.6744 (tttt) cc_final: 0.6422 (tttt) REVERT: B 341 VAL cc_start: 0.8318 (p) cc_final: 0.8116 (m) REVERT: B 349 HIS cc_start: 0.7969 (m-70) cc_final: 0.7132 (m170) REVERT: B 369 MET cc_start: 0.6781 (mtt) cc_final: 0.6543 (mtp) REVERT: B 387 LYS cc_start: 0.7448 (tmtm) cc_final: 0.7246 (tmtm) REVERT: E 10 ASP cc_start: 0.7053 (t70) cc_final: 0.6837 (t0) REVERT: E 126 ASP cc_start: 0.7648 (t70) cc_final: 0.7432 (m-30) REVERT: E 139 ARG cc_start: 0.7744 (ptm160) cc_final: 0.7532 (ptp-170) REVERT: E 172 ASP cc_start: 0.7591 (m-30) cc_final: 0.7312 (m-30) REVERT: E 250 VAL cc_start: 0.8834 (t) cc_final: 0.8607 (p) REVERT: E 316 VAL cc_start: 0.7350 (t) cc_final: 0.7144 (t) REVERT: E 328 LYS cc_start: 0.7065 (mmmt) cc_final: 0.6790 (mmmt) REVERT: E 349 HIS cc_start: 0.7728 (m-70) cc_final: 0.6960 (m170) REVERT: E 350 TYR cc_start: 0.8032 (m-80) cc_final: 0.7169 (m-10) REVERT: E 387 LYS cc_start: 0.7585 (tmtm) cc_final: 0.7227 (tmtm) REVERT: E 404 GLU cc_start: 0.7887 (mp0) cc_final: 0.7464 (mp0) REVERT: E 434 ASP cc_start: 0.7560 (m-30) cc_final: 0.7297 (t0) REVERT: E 436 LYS cc_start: 0.8282 (ptmt) cc_final: 0.8071 (pttt) REVERT: E 442 TYR cc_start: 0.7374 (t80) cc_final: 0.7132 (t80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.5410 time to fit residues: 132.9626 Evaluate side-chains 199 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN E 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119108 restraints weight = 14589.633| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3385 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11850 Z= 0.140 Angle : 0.498 7.161 16415 Z= 0.262 Chirality : 0.041 0.139 1834 Planarity : 0.004 0.050 1866 Dihedral : 13.397 94.507 2364 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.75 % Allowed : 10.29 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.02 (0.24), residues: 1260 helix: 0.55 (0.29), residues: 318 sheet: -0.59 (0.43), residues: 144 loop : -0.00 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.012 0.001 TYR E 488 PHE 0.014 0.002 PHE E 380 TRP 0.010 0.001 TRP B 348 HIS 0.008 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11810) covalent geometry : angle 0.48657 / 0.26 (16382) hydrogen bonds : bond 0.04535 / 3.07 ( 412) hydrogen bonds : angle 4.37238 / 3.15 ( 1077) metal coordination : bond 0.01061 / 0.65 ( 40) metal coordination : angle 2.38321 / 1.68 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8526 (mmp) cc_final: 0.8257 (mmm) REVERT: B 92 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7415 (mp0) REVERT: B 97 SER cc_start: 0.8262 (p) cc_final: 0.7994 (m) REVERT: B 164 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7964 (mtt90) REVERT: B 172 ASP cc_start: 0.7492 (m-30) cc_final: 0.7142 (m-30) REVERT: B 304 LYS cc_start: 0.7523 (tttp) cc_final: 0.7291 (tttm) REVERT: B 328 LYS cc_start: 0.6966 (tttt) cc_final: 0.6643 (tttt) REVERT: B 341 VAL cc_start: 0.8494 (p) cc_final: 0.8281 (m) REVERT: B 346 VAL cc_start: 0.8419 (m) cc_final: 0.8177 (t) REVERT: B 501 SER cc_start: 0.8500 (m) cc_final: 0.8225 (m) REVERT: E 172 ASP cc_start: 0.7604 (m-30) cc_final: 0.7385 (m-30) REVERT: E 302 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: E 316 VAL cc_start: 0.7981 (t) cc_final: 0.7772 (t) REVERT: E 387 LYS cc_start: 0.7612 (tmtm) cc_final: 0.7377 (tmtm) REVERT: E 404 GLU cc_start: 0.7848 (mp0) cc_final: 0.7539 (mp0) outliers start: 19 outliers final: 6 residues processed: 199 average time/residue: 0.5912 time to fit residues: 127.3045 Evaluate side-chains 199 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 369 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN B 418 ASN E 108 GLN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118303 restraints weight = 14690.751| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.98 r_work: 0.3379 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11850 Z= 0.151 Angle : 0.498 8.648 16415 Z= 0.261 Chirality : 0.041 0.188 1834 Planarity : 0.004 0.046 1866 Dihedral : 13.352 95.517 2364 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.57 % Allowed : 10.75 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.23 (0.23), residues: 1260 helix: 0.49 (0.29), residues: 330 sheet: -0.72 (0.42), residues: 144 loop : -0.26 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 433 TYR 0.015 0.001 TYR E 488 PHE 0.014 0.002 PHE E 432 TRP 0.011 0.001 TRP B 381 HIS 0.008 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11810) covalent geometry : angle 0.48601 / 0.26 (16382) hydrogen bonds : bond 0.04464 / 2.98 ( 412) hydrogen bonds : angle 4.27096 / 3.08 ( 1077) metal coordination : bond 0.01142 / 0.69 ( 40) metal coordination : angle 2.51388 / 1.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7717 (mt0) REVERT: B 92 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7481 (mp0) REVERT: B 97 SER cc_start: 0.8270 (p) cc_final: 0.8016 (m) REVERT: B 132 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (ptm) REVERT: B 172 ASP cc_start: 0.7512 (m-30) cc_final: 0.7151 (m-30) REVERT: B 328 LYS cc_start: 0.6992 (tttt) cc_final: 0.6659 (tttt) REVERT: B 341 VAL cc_start: 0.8534 (p) cc_final: 0.8302 (m) REVERT: B 346 VAL cc_start: 0.8439 (m) cc_final: 0.8200 (t) REVERT: E 172 ASP cc_start: 0.7601 (m-30) cc_final: 0.7354 (m-30) REVERT: E 302 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: E 316 VAL cc_start: 0.7988 (t) cc_final: 0.7780 (t) REVERT: E 349 HIS cc_start: 0.8022 (m-70) cc_final: 0.7719 (m170) REVERT: E 400 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7140 (mtm180) REVERT: E 404 GLU cc_start: 0.7843 (mp0) cc_final: 0.7536 (mp0) outliers start: 28 outliers final: 10 residues processed: 202 average time/residue: 0.5952 time to fit residues: 130.1565 Evaluate side-chains 199 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 80 HIS B 418 ASN E 108 GLN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118447 restraints weight = 14635.715| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.97 r_work: 0.3381 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11850 Z= 0.142 Angle : 0.493 11.868 16415 Z= 0.257 Chirality : 0.041 0.147 1834 Planarity : 0.004 0.045 1866 Dihedral : 13.372 95.363 2364 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.21 % Allowed : 11.40 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.18 (0.23), residues: 1260 helix: 0.78 (0.29), residues: 318 sheet: -0.75 (0.41), residues: 156 loop : -0.30 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 164 TYR 0.013 0.001 TYR E 488 PHE 0.011 0.001 PHE E 380 TRP 0.011 0.001 TRP B 381 HIS 0.011 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11810) covalent geometry : angle 0.48248 / 0.26 (16382) hydrogen bonds : bond 0.04152 / 2.77 ( 412) hydrogen bonds : angle 4.24033 / 3.06 ( 1077) metal coordination : bond 0.01085 / 0.64 ( 40) metal coordination : angle 2.34403 / 1.65 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8101 (m110) cc_final: 0.7774 (m110) REVERT: B 82 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7776 (mt0) REVERT: B 132 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8190 (ptm) REVERT: B 164 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7819 (mtt90) REVERT: B 172 ASP cc_start: 0.7489 (m-30) cc_final: 0.7145 (m-30) REVERT: B 328 LYS cc_start: 0.6985 (tttt) cc_final: 0.6647 (tttt) REVERT: B 341 VAL cc_start: 0.8531 (p) cc_final: 0.8305 (m) REVERT: B 346 VAL cc_start: 0.8453 (m) cc_final: 0.8214 (t) REVERT: E 172 ASP cc_start: 0.7603 (m-30) cc_final: 0.7355 (m-30) REVERT: E 302 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: E 316 VAL cc_start: 0.8034 (t) cc_final: 0.7829 (t) REVERT: E 349 HIS cc_start: 0.7997 (m-70) cc_final: 0.7736 (m170) REVERT: E 377 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7657 (tp) REVERT: E 400 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7082 (mtm180) REVERT: E 404 GLU cc_start: 0.7839 (mp0) cc_final: 0.7519 (mp0) outliers start: 24 outliers final: 9 residues processed: 183 average time/residue: 0.6098 time to fit residues: 120.1999 Evaluate side-chains 187 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118706 restraints weight = 14566.493| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.97 r_work: 0.3386 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11850 Z= 0.131 Angle : 0.481 11.603 16415 Z= 0.251 Chirality : 0.040 0.146 1834 Planarity : 0.004 0.048 1866 Dihedral : 13.399 94.984 2364 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.76 % Allowed : 11.58 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.08 (0.23), residues: 1260 helix: 0.88 (0.30), residues: 324 sheet: -0.75 (0.41), residues: 156 loop : -0.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 164 TYR 0.011 0.001 TYR E 488 PHE 0.011 0.001 PHE E 380 TRP 0.011 0.001 TRP B 381 HIS 0.011 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11810) covalent geometry : angle 0.47134 / 0.25 (16382) hydrogen bonds : bond 0.03955 / 2.63 ( 412) hydrogen bonds : angle 4.21009 / 3.04 ( 1077) metal coordination : bond 0.01012 / 0.59 ( 40) metal coordination : angle 2.19463 / 1.55 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8113 (m110) cc_final: 0.7768 (m110) REVERT: B 82 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7789 (mt0) REVERT: B 132 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8202 (ptm) REVERT: B 172 ASP cc_start: 0.7489 (m-30) cc_final: 0.7124 (m-30) REVERT: B 328 LYS cc_start: 0.6979 (tttt) cc_final: 0.6629 (tttt) REVERT: B 341 VAL cc_start: 0.8542 (p) cc_final: 0.8307 (m) REVERT: B 346 VAL cc_start: 0.8468 (m) cc_final: 0.8222 (t) REVERT: E 39 LEU cc_start: 0.8108 (mt) cc_final: 0.7907 (mm) REVERT: E 139 ARG cc_start: 0.8119 (ptp-170) cc_final: 0.7873 (ptp-170) REVERT: E 172 ASP cc_start: 0.7626 (m-30) cc_final: 0.7372 (m-30) REVERT: E 302 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: E 316 VAL cc_start: 0.7975 (t) cc_final: 0.7773 (t) REVERT: E 331 ASP cc_start: 0.7870 (t0) cc_final: 0.7556 (t0) REVERT: E 349 HIS cc_start: 0.7964 (m-70) cc_final: 0.7723 (m170) REVERT: E 377 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7642 (tp) REVERT: E 397 PHE cc_start: 0.8630 (t80) cc_final: 0.8174 (t80) REVERT: E 404 GLU cc_start: 0.7824 (mp0) cc_final: 0.7507 (mp0) outliers start: 30 outliers final: 11 residues processed: 187 average time/residue: 0.6094 time to fit residues: 122.9819 Evaluate side-chains 191 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 405 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119012 restraints weight = 14570.103| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.97 r_work: 0.3392 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11850 Z= 0.126 Angle : 0.471 10.751 16415 Z= 0.246 Chirality : 0.040 0.147 1834 Planarity : 0.004 0.041 1866 Dihedral : 13.402 94.685 2364 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.30 % Allowed : 12.22 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.05 (0.23), residues: 1260 helix: 0.93 (0.30), residues: 324 sheet: -0.74 (0.41), residues: 156 loop : -0.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 164 TYR 0.012 0.001 TYR E 488 PHE 0.011 0.001 PHE E 380 TRP 0.010 0.001 TRP B 381 HIS 0.010 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11810) covalent geometry : angle 0.46220 / 0.25 (16382) hydrogen bonds : bond 0.03843 / 2.56 ( 412) hydrogen bonds : angle 4.17304 / 3.01 ( 1077) metal coordination : bond 0.00955 / 0.55 ( 40) metal coordination : angle 2.12358 / 1.50 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8123 (m110) cc_final: 0.7781 (m110) REVERT: B 82 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7802 (mt0) REVERT: B 172 ASP cc_start: 0.7479 (m-30) cc_final: 0.7098 (m-30) REVERT: B 328 LYS cc_start: 0.6981 (tttt) cc_final: 0.6622 (tttt) REVERT: B 341 VAL cc_start: 0.8549 (p) cc_final: 0.8310 (m) REVERT: B 346 VAL cc_start: 0.8494 (m) cc_final: 0.8231 (t) REVERT: E 39 LEU cc_start: 0.8132 (mt) cc_final: 0.7912 (mm) REVERT: E 139 ARG cc_start: 0.8089 (ptp-170) cc_final: 0.7851 (ptp-170) REVERT: E 172 ASP cc_start: 0.7630 (m-30) cc_final: 0.7393 (m-30) REVERT: E 302 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: E 316 VAL cc_start: 0.7969 (t) cc_final: 0.7765 (t) REVERT: E 331 ASP cc_start: 0.7833 (t0) cc_final: 0.7523 (t0) REVERT: E 349 HIS cc_start: 0.7912 (m-70) cc_final: 0.7683 (m170) REVERT: E 377 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7653 (tp) REVERT: E 397 PHE cc_start: 0.8619 (t80) cc_final: 0.8179 (t80) REVERT: E 404 GLU cc_start: 0.7824 (mp0) cc_final: 0.7498 (mp0) outliers start: 25 outliers final: 12 residues processed: 192 average time/residue: 0.5765 time to fit residues: 119.2561 Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 405 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN A 80 HIS D 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.148352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117804 restraints weight = 14550.461| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.97 r_work: 0.3370 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11850 Z= 0.204 Angle : 0.534 11.814 16415 Z= 0.276 Chirality : 0.042 0.159 1834 Planarity : 0.005 0.049 1866 Dihedral : 13.455 97.382 2364 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.76 % Allowed : 12.41 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.26 (0.23), residues: 1260 helix: 0.67 (0.29), residues: 322 sheet: -0.83 (0.41), residues: 156 loop : -0.34 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 164 TYR 0.016 0.001 TYR B 330 PHE 0.016 0.002 PHE B 432 TRP 0.011 0.002 TRP E 381 HIS 0.010 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (11810) covalent geometry : angle 0.52129 / 0.27 (16382) hydrogen bonds : bond 0.04450 / 2.97 ( 412) hydrogen bonds : angle 4.31815 / 3.12 ( 1077) metal coordination : bond 0.01328 / 0.82 ( 40) metal coordination : angle 2.64250 / 1.88 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8163 (m110) cc_final: 0.7829 (m110) REVERT: B 82 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7783 (mt0) REVERT: B 172 ASP cc_start: 0.7467 (m-30) cc_final: 0.7115 (m-30) REVERT: B 246 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: B 328 LYS cc_start: 0.6957 (tttt) cc_final: 0.6481 (tttt) REVERT: B 329 VAL cc_start: 0.7935 (t) cc_final: 0.7625 (p) REVERT: B 331 ASP cc_start: 0.7787 (t0) cc_final: 0.7509 (t0) REVERT: B 341 VAL cc_start: 0.8579 (p) cc_final: 0.8314 (m) REVERT: B 378 CYS cc_start: 0.8217 (m) cc_final: 0.7910 (m) REVERT: E 39 LEU cc_start: 0.8218 (mt) cc_final: 0.7984 (mm) REVERT: E 139 ARG cc_start: 0.8124 (ptp-170) cc_final: 0.7822 (ptp-170) REVERT: E 172 ASP cc_start: 0.7582 (m-30) cc_final: 0.7368 (m-30) REVERT: E 271 SER cc_start: 0.8029 (p) cc_final: 0.7679 (m) REVERT: E 302 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: E 316 VAL cc_start: 0.7981 (t) cc_final: 0.7776 (t) REVERT: E 331 ASP cc_start: 0.7867 (t0) cc_final: 0.7552 (t0) REVERT: E 349 HIS cc_start: 0.7964 (m-70) cc_final: 0.7738 (m170) REVERT: E 377 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7675 (tp) REVERT: E 397 PHE cc_start: 0.8607 (t80) cc_final: 0.8205 (t80) REVERT: E 404 GLU cc_start: 0.7862 (mp0) cc_final: 0.7502 (mp0) outliers start: 30 outliers final: 10 residues processed: 196 average time/residue: 0.5155 time to fit residues: 109.3873 Evaluate side-chains 200 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 0.0060 chunk 44 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 65 GLN B 418 ASN E 108 GLN E 301 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119412 restraints weight = 14473.273| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.97 r_work: 0.3390 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11850 Z= 0.116 Angle : 0.480 11.331 16415 Z= 0.251 Chirality : 0.040 0.184 1834 Planarity : 0.004 0.044 1866 Dihedral : 13.397 95.264 2364 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 13.14 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.16 (0.23), residues: 1260 helix: 0.83 (0.30), residues: 322 sheet: -0.84 (0.41), residues: 156 loop : -0.29 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 164 TYR 0.017 0.001 TYR E 488 PHE 0.010 0.001 PHE B 432 TRP 0.012 0.001 TRP B 381 HIS 0.009 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11810) covalent geometry : angle 0.47119 / 0.25 (16382) hydrogen bonds : bond 0.03771 / 2.52 ( 412) hydrogen bonds : angle 4.22548 / 3.05 ( 1077) metal coordination : bond 0.00944 / 0.53 ( 40) metal coordination : angle 2.13060 / 1.48 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8125 (m110) cc_final: 0.7780 (m110) REVERT: B 82 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7796 (mt0) REVERT: B 172 ASP cc_start: 0.7471 (m-30) cc_final: 0.7109 (m-30) REVERT: B 246 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: B 249 TYR cc_start: 0.8250 (m-10) cc_final: 0.7972 (m-10) REVERT: B 328 LYS cc_start: 0.6998 (tttt) cc_final: 0.6577 (tttt) REVERT: B 329 VAL cc_start: 0.7936 (t) cc_final: 0.7651 (p) REVERT: B 331 ASP cc_start: 0.7768 (t0) cc_final: 0.7487 (t0) REVERT: B 341 VAL cc_start: 0.8578 (p) cc_final: 0.8309 (m) REVERT: B 378 CYS cc_start: 0.8199 (m) cc_final: 0.7896 (m) REVERT: B 387 LYS cc_start: 0.7674 (tmtm) cc_final: 0.7403 (tppp) REVERT: E 39 LEU cc_start: 0.8221 (mt) cc_final: 0.7977 (mm) REVERT: E 139 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7791 (ptp-170) REVERT: E 172 ASP cc_start: 0.7602 (m-30) cc_final: 0.7355 (m-30) REVERT: E 302 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: E 316 VAL cc_start: 0.7969 (t) cc_final: 0.7759 (t) REVERT: E 331 ASP cc_start: 0.7793 (t0) cc_final: 0.7474 (t0) REVERT: E 349 HIS cc_start: 0.7909 (m-70) cc_final: 0.7677 (m170) REVERT: E 377 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7640 (tp) REVERT: E 397 PHE cc_start: 0.8582 (t80) cc_final: 0.8194 (t80) REVERT: E 404 GLU cc_start: 0.7844 (mp0) cc_final: 0.7483 (mp0) REVERT: E 434 ASP cc_start: 0.7638 (t0) cc_final: 0.7399 (t0) outliers start: 22 outliers final: 9 residues processed: 192 average time/residue: 0.5686 time to fit residues: 117.7487 Evaluate side-chains 198 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 405 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118782 restraints weight = 14382.803| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.96 r_work: 0.3384 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11850 Z= 0.160 Angle : 0.501 11.374 16415 Z= 0.260 Chirality : 0.041 0.157 1834 Planarity : 0.004 0.054 1866 Dihedral : 13.409 96.138 2364 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.84 % Allowed : 13.60 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.23 (0.23), residues: 1260 helix: 0.75 (0.30), residues: 322 sheet: -0.90 (0.40), residues: 156 loop : -0.32 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 164 TYR 0.017 0.001 TYR E 488 PHE 0.013 0.001 PHE B 432 TRP 0.011 0.001 TRP B 381 HIS 0.008 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (11810) covalent geometry : angle 0.49024 / 0.26 (16382) hydrogen bonds : bond 0.04029 / 2.69 ( 412) hydrogen bonds : angle 4.24409 / 3.06 ( 1077) metal coordination : bond 0.01087 / 0.64 ( 40) metal coordination : angle 2.33753 / 1.66 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8144 (m110) cc_final: 0.7805 (m110) REVERT: B 82 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7778 (mt0) REVERT: B 172 ASP cc_start: 0.7466 (m-30) cc_final: 0.7102 (m-30) REVERT: B 246 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: B 328 LYS cc_start: 0.6948 (tttt) cc_final: 0.6533 (tttt) REVERT: B 329 VAL cc_start: 0.8017 (t) cc_final: 0.7783 (p) REVERT: B 331 ASP cc_start: 0.7821 (t0) cc_final: 0.7522 (t0) REVERT: B 341 VAL cc_start: 0.8582 (p) cc_final: 0.8310 (m) REVERT: B 378 CYS cc_start: 0.8213 (m) cc_final: 0.7906 (m) REVERT: E 55 ILE cc_start: 0.8325 (mm) cc_final: 0.8104 (mm) REVERT: E 139 ARG cc_start: 0.8082 (ptp-170) cc_final: 0.7791 (ptp-170) REVERT: E 172 ASP cc_start: 0.7608 (m-30) cc_final: 0.7380 (m-30) REVERT: E 302 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: E 316 VAL cc_start: 0.8002 (t) cc_final: 0.7793 (t) REVERT: E 331 ASP cc_start: 0.7806 (t0) cc_final: 0.7510 (t0) REVERT: E 349 HIS cc_start: 0.7921 (m-70) cc_final: 0.7685 (m170) REVERT: E 377 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7654 (tp) REVERT: E 397 PHE cc_start: 0.8567 (t80) cc_final: 0.8201 (t80) REVERT: E 404 GLU cc_start: 0.7861 (mp0) cc_final: 0.7499 (mp0) REVERT: E 434 ASP cc_start: 0.7655 (t0) cc_final: 0.7406 (t0) outliers start: 20 outliers final: 9 residues processed: 191 average time/residue: 0.5609 time to fit residues: 115.5647 Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119295 restraints weight = 14553.935| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.98 r_work: 0.3391 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11850 Z= 0.118 Angle : 0.481 11.230 16415 Z= 0.250 Chirality : 0.040 0.150 1834 Planarity : 0.004 0.049 1866 Dihedral : 13.380 94.963 2364 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.75 % Allowed : 13.69 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.15 (0.23), residues: 1260 helix: 0.85 (0.30), residues: 322 sheet: -0.92 (0.40), residues: 156 loop : -0.27 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 164 TYR 0.023 0.001 TYR E 488 PHE 0.010 0.001 PHE E 380 TRP 0.010 0.001 TRP B 381 HIS 0.009 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11810) covalent geometry : angle 0.47226 / 0.25 (16382) hydrogen bonds : bond 0.03725 / 2.49 ( 412) hydrogen bonds : angle 4.21682 / 3.04 ( 1077) metal coordination : bond 0.00922 / 0.52 ( 40) metal coordination : angle 2.03697 / 1.43 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8121 (m110) cc_final: 0.7780 (m110) REVERT: B 82 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7774 (mt0) REVERT: B 172 ASP cc_start: 0.7479 (m-30) cc_final: 0.7110 (m-30) REVERT: B 328 LYS cc_start: 0.6934 (tttt) cc_final: 0.6514 (tttt) REVERT: B 329 VAL cc_start: 0.8041 (t) cc_final: 0.7812 (p) REVERT: B 331 ASP cc_start: 0.7750 (t0) cc_final: 0.7467 (t0) REVERT: B 341 VAL cc_start: 0.8574 (p) cc_final: 0.8308 (m) REVERT: B 378 CYS cc_start: 0.8193 (m) cc_final: 0.7893 (m) REVERT: E 55 ILE cc_start: 0.8313 (mm) cc_final: 0.8092 (mm) REVERT: E 139 ARG cc_start: 0.8041 (ptp-170) cc_final: 0.7767 (ptp-170) REVERT: E 172 ASP cc_start: 0.7619 (m-30) cc_final: 0.7394 (m-30) REVERT: E 302 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: E 316 VAL cc_start: 0.8003 (t) cc_final: 0.7786 (t) REVERT: E 331 ASP cc_start: 0.7733 (t0) cc_final: 0.7430 (t0) REVERT: E 349 HIS cc_start: 0.7914 (m-70) cc_final: 0.7674 (m170) REVERT: E 377 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7638 (tp) REVERT: E 397 PHE cc_start: 0.8553 (t80) cc_final: 0.8206 (t80) REVERT: E 404 GLU cc_start: 0.7853 (mp0) cc_final: 0.7488 (mp0) REVERT: E 434 ASP cc_start: 0.7643 (t0) cc_final: 0.7430 (t0) outliers start: 19 outliers final: 11 residues processed: 190 average time/residue: 0.5342 time to fit residues: 109.4869 Evaluate side-chains 194 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 405 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 65 GLN E 108 GLN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118406 restraints weight = 14549.964| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3385 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11850 Z= 0.144 Angle : 0.503 12.875 16415 Z= 0.260 Chirality : 0.040 0.154 1834 Planarity : 0.004 0.060 1866 Dihedral : 13.385 95.218 2364 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.65 % Allowed : 13.79 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.20 (0.23), residues: 1260 helix: 0.78 (0.30), residues: 322 sheet: -0.93 (0.40), residues: 156 loop : -0.29 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 164 TYR 0.025 0.001 TYR E 488 PHE 0.014 0.001 PHE B 432 TRP 0.007 0.001 TRP E 227 HIS 0.009 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11810) covalent geometry : angle 0.49379 / 0.26 (16382) hydrogen bonds : bond 0.03859 / 2.59 ( 412) hydrogen bonds : angle 4.23337 / 3.05 ( 1077) metal coordination : bond 0.00991 / 0.58 ( 40) metal coordination : angle 2.17957 / 1.55 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.07 seconds wall clock time: 70 minutes 12.36 seconds (4212.36 seconds total)