Starting phenix.real_space_refine on Wed Aug 5 20:01:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycl_72776/08_2026/9ycl_72776.map" } resolution = 2.5 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= 0.000 sd= 0.015 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 62 5.49 5 Mg 2 5.21 5 S 88 5.16 5 C 6932 2.51 5 N 1922 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 11282 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: {'PTRANS': 28, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 655 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} 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: {'PTRANS': 28, 'TRANS': 476} Chain breaks: 1 Chain: "F" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 655 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} 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 33.099 81.316 83.968 1.00 40.36 S ATOM 553 SG CYS A 77 36.433 80.525 82.254 1.00 39.18 S ATOM 651 SG CYS A 90 33.207 80.257 80.298 1.00 47.23 S ATOM 859 SG CYS A 117 15.371 86.674 74.596 1.00 92.08 S ATOM 880 SG CYS A 120 16.685 89.601 72.821 1.00 84.42 S ATOM 949 SG CYS A 128 14.477 90.180 75.809 1.00 88.93 S ATOM 963 SG CYS A 130 12.857 89.033 72.662 1.00103.21 S ATOM 1498 SG CYS D 74 34.512 42.713 85.518 1.00 41.22 S ATOM 1524 SG CYS D 77 38.209 42.826 86.622 1.00 41.50 S ATOM 1622 SG CYS D 90 35.389 43.651 89.155 1.00 50.93 S ATOM 1830 SG CYS D 117 17.690 39.716 97.399 1.00100.55 S ATOM 1851 SG CYS D 120 18.640 36.420 98.825 1.00 93.38 S ATOM 1920 SG CYS D 128 16.047 36.657 96.011 1.00 98.60 S ATOM 1934 SG CYS D 130 15.102 37.615 99.517 1.00109.21 S ATOM 3547 SG CYS B 207 22.633 61.570 108.527 1.00 48.63 S ATOM 3567 SG CYS B 210 21.596 60.692 112.044 1.00 54.09 S ATOM 3689 SG CYS B 226 25.192 60.074 110.999 1.00 55.04 S ATOM 3988 SG CYS B 261 56.431 60.371 121.910 1.00 49.51 S ATOM 4118 SG CYS B 279 53.431 62.740 121.212 1.00 56.83 S ATOM 5493 SG CYS B 448 23.483 38.803 157.579 1.00198.92 S ATOM 5576 SG CYS B 474 24.874 35.661 156.064 1.00199.75 S ATOM 5618 SG CYS B 481 22.192 37.603 154.134 1.00202.09 S ATOM 8211 SG CYS E 207 23.994 65.729 64.394 1.00 45.67 S ATOM 8231 SG CYS E 210 22.776 67.022 61.030 1.00 57.50 S ATOM 8353 SG CYS E 226 26.471 67.024 61.710 1.00 45.72 S ATOM 8652 SG CYS E 261 55.144 62.952 45.675 1.00 62.58 S ATOM 8782 SG CYS E 279 51.999 61.067 46.910 1.00 59.72 S ATOM 10157 SG CYS E 448 21.399 92.826 17.412 1.00206.19 S ATOM 10240 SG CYS E 474 23.544 95.354 18.824 1.00208.97 S ATOM 10282 SG CYS E 481 20.915 93.710 21.128 1.00203.11 S Time building chain proxies: 2.16, per 1000 atoms: 0.19 Number of scatterers: 11282 At special positions: 0 Unit cell: (80.5061, 122.509, 172.388, 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 62 15.00 Mg 2 11.99 O 2266 8.00 N 1922 7.00 C 6932 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: 0.83 Conformation dependent library (CDL) restraints added in 349.4 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 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " 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 279 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " 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 77 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 74 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 90 " 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 117 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 130 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" ND1 HIS E 229 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 210 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 226 " 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 481 " pdb="ZN ZN E 604 " - pdb=" SG CYS E 448 " 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: 40 helices and 16 sheets defined 30.9% alpha, 16.6% beta 30 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.505A pdb=" N LEU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 80 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 113 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.531A pdb=" N LEU D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 33 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.812A pdb=" N ARG B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 155 removed outlier: 5.088A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.746A pdb=" N HIS B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.611A pdb=" N ARG B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.486A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.816A 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 259 removed outlier: 3.525A pdb=" N ASN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 302 through 323 removed outlier: 3.673A pdb=" N SER B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.800A pdb=" N ALA B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 472 through 477 removed outlier: 4.228A pdb=" N GLY B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 502 removed outlier: 3.992A pdb=" N GLU B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.620A pdb=" N ASN B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 75 through 82 Processing helix chain 'E' and resid 143 through 155 removed outlier: 5.216A pdb=" N HIS E 148 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 158 through 175 removed outlier: 3.975A pdb=" N ARG E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 removed outlier: 4.481A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 252 through 261 removed outlier: 4.158A pdb=" N TYR E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 302 through 323 Processing helix chain 'E' and resid 367 through 371 removed outlier: 4.140A pdb=" N ALA E 370 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER E 371 " --> pdb=" O ASP E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing helix chain 'E' and resid 428 through 433 removed outlier: 3.827A pdb=" N ARG E 433 " --> pdb=" O SER E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 502 removed outlier: 3.842A pdb=" N GLU E 487 " --> pdb=" O LYS E 483 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 502 " --> pdb=" O VAL E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 519 removed outlier: 3.735A pdb=" N ASN E 515 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 55 removed outlier: 4.336A pdb=" N VAL B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.001A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.001A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 351 removed outlier: 6.622A pdb=" N LYS B 328 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 379 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR B 330 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TRP B 381 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 332 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 6.301A pdb=" N TYR B 442 " --> pdb=" O ILE B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 52 through 55 removed outlier: 4.295A pdb=" N VAL E 124 " --> pdb=" O ILE E 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 116 through 118 removed outlier: 6.957A pdb=" N ASN E 104 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E 96 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA E 94 " --> pdb=" O PRO E 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 116 through 118 removed outlier: 6.957A pdb=" N ASN E 104 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E 96 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA E 94 " --> pdb=" O PRO E 106 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE E 87 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'E' and resid 347 through 351 removed outlier: 6.608A pdb=" N LYS E 328 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU E 379 " --> pdb=" O LYS E 328 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR E 330 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TRP E 381 " --> pdb=" O TYR E 330 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE E 332 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 406 through 408 Processing sheet with id=AB7, first strand: chain 'E' and resid 442 through 443 removed outlier: 6.149A pdb=" N TYR E 442 " --> pdb=" O ILE E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 334 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.05 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: 3157 1.34 - 1.46: 2654 1.46 - 1.57: 5663 1.57 - 1.69: 120 1.69 - 1.81: 106 Bond restraints: 11700 Sorted by residual: bond pdb=" N ILE E 294 " pdb=" CA ILE E 294 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.37e+00 bond pdb=" N VAL B 125 " pdb=" CA VAL B 125 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.26e+00 bond pdb=" N VAL E 269 " pdb=" CA VAL E 269 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.11e-02 8.12e+03 8.62e+00 bond pdb=" N ILE B 340 " pdb=" CA ILE B 340 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.23e+00 bond pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 7.89e+00 ... (remaining 11695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 15314 1.70 - 3.39: 802 3.39 - 5.09: 68 5.09 - 6.79: 19 6.79 - 8.49: 3 Bond angle restraints: 16206 Sorted by residual: angle pdb=" CA VAL E 269 " pdb=" C VAL E 269 " pdb=" O VAL E 269 " ideal model delta sigma weight residual 121.63 117.69 3.94 9.90e-01 1.02e+00 1.58e+01 angle pdb=" N GLY B 130 " pdb=" CA GLY B 130 " pdb=" C GLY B 130 " ideal model delta sigma weight residual 110.20 115.39 -5.19 1.32e+00 5.74e-01 1.55e+01 angle pdb=" C TYR E 365 " pdb=" N THR E 366 " pdb=" CA THR E 366 " ideal model delta sigma weight residual 121.90 116.96 4.94 1.26e+00 6.30e-01 1.53e+01 angle pdb=" CA VAL B 269 " pdb=" C VAL B 269 " pdb=" O VAL B 269 " ideal model delta sigma weight residual 121.67 117.82 3.85 1.02e+00 9.61e-01 1.42e+01 angle pdb=" N GLU A 6 " pdb=" CA GLU A 6 " pdb=" CB GLU A 6 " ideal model delta sigma weight residual 111.20 105.17 6.03 1.62e+00 3.81e-01 1.38e+01 ... (remaining 16201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6283 17.83 - 35.65: 453 35.65 - 53.48: 106 53.48 - 71.30: 68 71.30 - 89.13: 18 Dihedral angle restraints: 6928 sinusoidal: 3216 harmonic: 3712 Sorted by residual: dihedral pdb=" CA ASP E 368 " pdb=" C ASP E 368 " pdb=" N MET E 369 " pdb=" CA MET E 369 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLU B 367 " pdb=" C GLU B 367 " pdb=" N ASP B 368 " pdb=" CA ASP B 368 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU B 92 " pdb=" C GLU B 92 " pdb=" N GLY B 93 " pdb=" CA GLY B 93 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1680 0.114 - 0.227: 126 0.227 - 0.341: 2 0.341 - 0.454: 3 0.454 - 0.568: 5 Chirality restraints: 1816 Sorted by residual: chirality pdb=" P G F 7 " pdb=" OP1 G F 7 " pdb=" OP2 G F 7 " pdb=" O5' G F 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.05e+00 chirality pdb=" P G C 7 " pdb=" OP1 G C 7 " pdb=" OP2 G C 7 " pdb=" O5' G C 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P A F 8 " pdb=" OP1 A F 8 " pdb=" OP2 A F 8 " pdb=" O5' A F 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 1813 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 373 " -0.026 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE E 373 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE E 373 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 373 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 373 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE E 373 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 92 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" CD GLU B 92 " -0.046 2.00e-02 2.50e+03 pdb=" OE1 GLU B 92 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 92 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 273 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" CG ASP B 273 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP B 273 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 273 " 0.017 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 30 2.43 - 3.05: 6362 3.05 - 3.66: 17309 3.66 - 4.28: 26803 4.28 - 4.90: 42487 Nonbonded interactions: 92991 Sorted by model distance: nonbonded pdb=" OD2 ASP B 273 " pdb="MG MG B 601 " model vdw 1.808 2.170 nonbonded pdb=" OD2 ASP E 273 " pdb="MG MG E 601 " model vdw 1.904 2.170 nonbonded pdb=" OD2 ASP E 90 " pdb="MG MG E 601 " model vdw 2.127 2.170 nonbonded pdb=" OE2 GLU B 92 " pdb="MG MG B 601 " model vdw 2.153 2.170 nonbonded pdb=" OP1 C C 39 " pdb="MG MG B 601 " model vdw 2.192 2.170 ... (remaining 92986 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: 3.860 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.170 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11740 Z= 0.311 Angle : 0.802 10.566 16239 Z= 0.531 Chirality : 0.062 0.568 1816 Planarity : 0.006 0.089 1862 Dihedral : 15.056 89.129 4552 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1260 helix: -0.37 (0.26), residues: 304 sheet: 0.16 (0.38), residues: 180 loop : -0.39 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 372 TYR 0.028 0.002 TYR B 488 PHE 0.057 0.002 PHE E 373 TRP 0.012 0.001 TRP B 381 HIS 0.009 0.001 HIS E 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.31 (11700) covalent geometry : angle 0.78851 / 0.53 (16206) hydrogen bonds : bond 0.15615 / 10.01 ( 390) hydrogen bonds : angle 5.58380 / 3.98 ( 1007) metal coordination : bond 0.00949 / 0.62 ( 40) metal coordination : angle 3.37808 / 2.35 ( 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 228 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.8296 (tp) cc_final: 0.8020 (tp) REVERT: A 40 ASN cc_start: 0.8027 (t0) cc_final: 0.7776 (t0) REVERT: A 65 GLN cc_start: 0.8151 (mt0) cc_final: 0.7787 (mt0) REVERT: B 10 ASP cc_start: 0.7722 (t0) cc_final: 0.7487 (t0) REVERT: B 31 ASP cc_start: 0.8130 (m-30) cc_final: 0.7915 (m-30) REVERT: B 294 ILE cc_start: 0.8133 (mt) cc_final: 0.7765 (tt) REVERT: B 492 MET cc_start: 0.6503 (mmt) cc_final: 0.6247 (mmp) REVERT: E 2 GLN cc_start: 0.7553 (mt0) cc_final: 0.7318 (mt0) REVERT: E 126 ASP cc_start: 0.7734 (m-30) cc_final: 0.7533 (m-30) REVERT: E 258 ASP cc_start: 0.8217 (m-30) cc_final: 0.7960 (m-30) REVERT: E 338 ILE cc_start: 0.8800 (mm) cc_final: 0.7885 (mp) REVERT: E 398 ASP cc_start: 0.7489 (t70) cc_final: 0.7284 (t70) REVERT: E 498 VAL cc_start: 0.6362 (t) cc_final: 0.6151 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.5010 time to fit residues: 123.2307 Evaluate side-chains 210 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 98 GLN B 42 ASN E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123991 restraints weight = 14610.105| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.74 r_work: 0.3490 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11740 Z= 0.114 Angle : 0.500 6.663 16239 Z= 0.261 Chirality : 0.040 0.194 1816 Planarity : 0.004 0.039 1862 Dihedral : 12.217 73.676 2314 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.92 % Allowed : 13.14 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1260 helix: 0.38 (0.29), residues: 304 sheet: 0.21 (0.38), residues: 176 loop : -0.30 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.012 0.001 TYR B 365 PHE 0.015 0.001 PHE E 373 TRP 0.008 0.001 TRP E 186 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11700) covalent geometry : angle 0.48745 / 0.26 (16206) hydrogen bonds : bond 0.04756 / 3.36 ( 390) hydrogen bonds : angle 4.19903 / 3.02 ( 1007) metal coordination : bond 0.00703 / 0.50 ( 40) metal coordination : angle 2.48308 / 1.75 ( 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 238 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8413 (m110) cc_final: 0.8110 (m-40) REVERT: A 65 GLN cc_start: 0.8320 (mt0) cc_final: 0.7971 (mt0) REVERT: D 25 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7891 (tptp) REVERT: B 10 ASP cc_start: 0.7690 (t0) cc_final: 0.7438 (t0) REVERT: B 120 GLN cc_start: 0.8212 (mm110) cc_final: 0.7986 (mm110) REVERT: B 132 MET cc_start: 0.8167 (ttm) cc_final: 0.7907 (ttp) REVERT: B 294 ILE cc_start: 0.8317 (mt) cc_final: 0.7970 (tt) REVERT: B 492 MET cc_start: 0.7387 (mmt) cc_final: 0.7156 (mmp) REVERT: E 126 ASP cc_start: 0.7781 (m-30) cc_final: 0.7555 (m-30) REVERT: E 441 PHE cc_start: 0.8315 (p90) cc_final: 0.7912 (p90) outliers start: 10 outliers final: 4 residues processed: 232 average time/residue: 0.4786 time to fit residues: 119.8633 Evaluate side-chains 211 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain E residue 161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 93 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 0.0470 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 515 ASN E 131 ASN E 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.161538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122978 restraints weight = 14673.611| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.80 r_work: 0.3495 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11740 Z= 0.100 Angle : 0.470 6.792 16239 Z= 0.243 Chirality : 0.039 0.204 1816 Planarity : 0.004 0.059 1862 Dihedral : 12.069 73.716 2314 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 12.50 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1260 helix: 0.64 (0.29), residues: 306 sheet: 0.19 (0.40), residues: 154 loop : -0.31 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.013 0.001 TYR B 365 PHE 0.010 0.001 PHE B 397 TRP 0.015 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11700) covalent geometry : angle 0.45888 / 0.24 (16206) hydrogen bonds : bond 0.04150 / 2.97 ( 390) hydrogen bonds : angle 3.93767 / 2.83 ( 1007) metal coordination : bond 0.00643 / 0.44 ( 40) metal coordination : angle 2.26060 / 1.60 ( 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 236 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8476 (m110) cc_final: 0.8189 (m-40) REVERT: A 65 GLN cc_start: 0.8347 (mt0) cc_final: 0.7959 (mt0) REVERT: D 25 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7795 (tptp) REVERT: B 10 ASP cc_start: 0.7705 (t0) cc_final: 0.7432 (t0) REVERT: B 294 ILE cc_start: 0.8313 (mt) cc_final: 0.7936 (tt) REVERT: B 393 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6278 (pp) REVERT: B 406 ASN cc_start: 0.7733 (t0) cc_final: 0.7451 (t0) REVERT: B 492 MET cc_start: 0.7435 (mmt) cc_final: 0.7188 (mmp) REVERT: E 126 ASP cc_start: 0.7756 (m-30) cc_final: 0.7531 (m-30) REVERT: E 295 GLU cc_start: 0.8201 (tt0) cc_final: 0.7893 (mt-10) REVERT: E 441 PHE cc_start: 0.8341 (p90) cc_final: 0.7960 (p90) outliers start: 18 outliers final: 6 residues processed: 228 average time/residue: 0.5164 time to fit residues: 126.9759 Evaluate side-chains 224 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain E residue 231 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.9980 chunk 116 optimal weight: 0.0030 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 131 ASN E 246 GLN E 272 ASN E 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.161054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124025 restraints weight = 14735.525| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.79 r_work: 0.3481 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11740 Z= 0.108 Angle : 0.464 6.178 16239 Z= 0.241 Chirality : 0.039 0.155 1816 Planarity : 0.004 0.041 1862 Dihedral : 12.082 73.720 2314 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.47 % Allowed : 13.14 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1260 helix: 0.79 (0.29), residues: 306 sheet: 0.33 (0.43), residues: 140 loop : -0.28 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.015 0.001 TYR B 365 PHE 0.008 0.001 PHE B 397 TRP 0.014 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11700) covalent geometry : angle 0.45423 / 0.24 (16206) hydrogen bonds : bond 0.04010 / 2.86 ( 390) hydrogen bonds : angle 3.87706 / 2.79 ( 1007) metal coordination : bond 0.00687 / 0.45 ( 40) metal coordination : angle 2.19786 / 1.53 ( 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 233 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8515 (m110) cc_final: 0.8231 (m-40) REVERT: A 65 GLN cc_start: 0.8371 (mt0) cc_final: 0.8000 (mt0) REVERT: D 25 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7901 (tptp) REVERT: B 10 ASP cc_start: 0.7786 (t0) cc_final: 0.7526 (t0) REVERT: B 294 ILE cc_start: 0.8311 (mt) cc_final: 0.7921 (tt) REVERT: B 393 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6288 (pp) REVERT: B 492 MET cc_start: 0.7462 (mmt) cc_final: 0.7214 (mmp) REVERT: E 126 ASP cc_start: 0.7767 (m-30) cc_final: 0.7541 (m-30) REVERT: E 222 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: E 441 PHE cc_start: 0.8364 (p90) cc_final: 0.7969 (p90) outliers start: 16 outliers final: 7 residues processed: 224 average time/residue: 0.5171 time to fit residues: 125.1137 Evaluate side-chains 221 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 222 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 114 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 120 GLN B 406 ASN E 131 ASN E 246 GLN E 272 ASN E 515 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123017 restraints weight = 14674.167| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.73 r_work: 0.3498 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11740 Z= 0.112 Angle : 0.461 6.350 16239 Z= 0.239 Chirality : 0.039 0.197 1816 Planarity : 0.004 0.045 1862 Dihedral : 12.056 73.793 2314 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 13.24 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1260 helix: 0.82 (0.29), residues: 308 sheet: 0.17 (0.40), residues: 168 loop : -0.24 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.014 0.001 TYR B 365 PHE 0.016 0.001 PHE B 397 TRP 0.014 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (11700) covalent geometry : angle 0.45065 / 0.24 (16206) hydrogen bonds : bond 0.03935 / 2.81 ( 390) hydrogen bonds : angle 3.83823 / 2.77 ( 1007) metal coordination : bond 0.00684 / 0.44 ( 40) metal coordination : angle 2.21577 / 1.53 ( 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 232 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.264 Fit side-chains REVERT: A 32 ASN cc_start: 0.8516 (m110) cc_final: 0.8242 (m-40) REVERT: A 60 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 65 GLN cc_start: 0.8381 (mt0) cc_final: 0.8029 (mt0) REVERT: B 10 ASP cc_start: 0.7753 (t0) cc_final: 0.7482 (t0) REVERT: B 222 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: B 294 ILE cc_start: 0.8297 (mt) cc_final: 0.7911 (tt) REVERT: B 393 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6253 (pp) REVERT: B 492 MET cc_start: 0.7393 (mmt) cc_final: 0.7125 (mmt) REVERT: E 126 ASP cc_start: 0.7675 (m-30) cc_final: 0.7446 (m-30) REVERT: E 222 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: E 396 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7025 (ttt90) REVERT: E 441 PHE cc_start: 0.8348 (p90) cc_final: 0.7934 (p90) outliers start: 19 outliers final: 10 residues processed: 219 average time/residue: 0.5050 time to fit residues: 119.3948 Evaluate side-chains 227 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 ASN D 18 ASN B 42 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.159476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120602 restraints weight = 14569.436| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.63 r_work: 0.3478 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11740 Z= 0.170 Angle : 0.507 7.867 16239 Z= 0.261 Chirality : 0.041 0.164 1816 Planarity : 0.004 0.051 1862 Dihedral : 12.118 73.997 2314 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.02 % Allowed : 13.05 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1260 helix: 0.53 (0.29), residues: 316 sheet: 0.20 (0.41), residues: 158 loop : -0.37 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.015 0.002 TYR D 76 PHE 0.010 0.001 PHE B 73 TRP 0.021 0.001 TRP E 506 HIS 0.005 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (11700) covalent geometry : angle 0.49171 / 0.26 (16206) hydrogen bonds : bond 0.04500 / 3.20 ( 390) hydrogen bonds : angle 3.95270 / 2.85 ( 1007) metal coordination : bond 0.01071 / 0.64 ( 40) metal coordination : angle 2.76003 / 1.88 ( 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 241 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.287 Fit side-chains REVERT: A 65 GLN cc_start: 0.8479 (mt0) cc_final: 0.8145 (mt0) REVERT: B 10 ASP cc_start: 0.7783 (t0) cc_final: 0.7492 (t0) REVERT: B 222 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: B 294 ILE cc_start: 0.8326 (mt) cc_final: 0.7908 (tt) REVERT: B 393 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6294 (pp) REVERT: B 492 MET cc_start: 0.7427 (mmt) cc_final: 0.7158 (mmt) REVERT: E 126 ASP cc_start: 0.7684 (m-30) cc_final: 0.7457 (m-30) REVERT: E 128 GLU cc_start: 0.8336 (pm20) cc_final: 0.7811 (pm20) REVERT: E 396 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7040 (ttt90) REVERT: E 441 PHE cc_start: 0.8358 (p90) cc_final: 0.8034 (p90) REVERT: E 498 VAL cc_start: 0.7758 (t) cc_final: 0.7411 (p) outliers start: 22 outliers final: 10 residues processed: 230 average time/residue: 0.5095 time to fit residues: 126.8383 Evaluate side-chains 229 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 115 optimal weight: 0.0470 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.0050 chunk 11 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 ASN B 406 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122353 restraints weight = 14409.474| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.77 r_work: 0.3488 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11740 Z= 0.104 Angle : 0.465 7.675 16239 Z= 0.240 Chirality : 0.039 0.154 1816 Planarity : 0.004 0.045 1862 Dihedral : 12.057 73.810 2314 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.65 % Allowed : 14.06 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1260 helix: 0.83 (0.29), residues: 306 sheet: 0.19 (0.41), residues: 158 loop : -0.24 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.012 0.001 TYR B 365 PHE 0.024 0.001 PHE B 397 TRP 0.022 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11700) covalent geometry : angle 0.45023 / 0.24 (16206) hydrogen bonds : bond 0.03890 / 2.77 ( 390) hydrogen bonds : angle 3.85582 / 2.78 ( 1007) metal coordination : bond 0.00621 / 0.39 ( 40) metal coordination : angle 2.60318 / 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 238 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.287 Fit side-chains REVERT: A 32 ASN cc_start: 0.8535 (m110) cc_final: 0.8270 (m-40) REVERT: A 60 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 65 GLN cc_start: 0.8443 (mt0) cc_final: 0.8048 (mt0) REVERT: B 10 ASP cc_start: 0.7795 (t0) cc_final: 0.7491 (t0) REVERT: B 222 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: B 294 ILE cc_start: 0.8307 (mt) cc_final: 0.7893 (tt) REVERT: B 393 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6226 (pp) REVERT: B 492 MET cc_start: 0.7445 (mmt) cc_final: 0.7171 (mmt) REVERT: E 126 ASP cc_start: 0.7674 (m-30) cc_final: 0.7465 (m-30) REVERT: E 128 GLU cc_start: 0.8336 (pm20) cc_final: 0.7806 (pm20) REVERT: E 396 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7085 (ttt90) REVERT: E 441 PHE cc_start: 0.8364 (p90) cc_final: 0.8032 (p90) outliers start: 18 outliers final: 9 residues processed: 227 average time/residue: 0.4925 time to fit residues: 121.0253 Evaluate side-chains 232 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 20 optimal weight: 0.0670 chunk 126 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.160699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122527 restraints weight = 14370.923| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.71 r_work: 0.3493 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11740 Z= 0.121 Angle : 0.469 7.089 16239 Z= 0.242 Chirality : 0.039 0.154 1816 Planarity : 0.004 0.046 1862 Dihedral : 12.065 73.844 2314 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 14.25 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1260 helix: 0.83 (0.29), residues: 304 sheet: 0.23 (0.41), residues: 158 loop : -0.22 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.013 0.001 TYR B 365 PHE 0.008 0.001 PHE E 73 TRP 0.028 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11700) covalent geometry : angle 0.45620 / 0.24 (16206) hydrogen bonds : bond 0.03961 / 2.83 ( 390) hydrogen bonds : angle 3.87165 / 2.79 ( 1007) metal coordination : bond 0.00784 / 0.47 ( 40) metal coordination : angle 2.43643 / 1.70 ( 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 238 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.264 Fit side-chains REVERT: A 32 ASN cc_start: 0.8529 (m110) cc_final: 0.8265 (m-40) REVERT: A 60 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 65 GLN cc_start: 0.8441 (mt0) cc_final: 0.8048 (mt0) REVERT: B 10 ASP cc_start: 0.7795 (t0) cc_final: 0.7501 (t0) REVERT: B 294 ILE cc_start: 0.8310 (mt) cc_final: 0.7892 (tt) REVERT: B 393 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6209 (pp) REVERT: B 492 MET cc_start: 0.7409 (mmt) cc_final: 0.7133 (mmt) REVERT: E 126 ASP cc_start: 0.7642 (m-30) cc_final: 0.7424 (m-30) REVERT: E 334 ASN cc_start: 0.7091 (m110) cc_final: 0.6572 (m-40) REVERT: E 396 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7002 (ttt90) REVERT: E 441 PHE cc_start: 0.8383 (p90) cc_final: 0.8034 (p90) REVERT: E 503 PHE cc_start: 0.8824 (m-80) cc_final: 0.8588 (m-80) outliers start: 17 outliers final: 10 residues processed: 231 average time/residue: 0.4472 time to fit residues: 112.0999 Evaluate side-chains 227 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 ASN B 406 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.160501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121226 restraints weight = 14341.041| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.63 r_work: 0.3482 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11740 Z= 0.133 Angle : 0.480 7.317 16239 Z= 0.248 Chirality : 0.040 0.153 1816 Planarity : 0.004 0.047 1862 Dihedral : 12.073 73.902 2314 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.65 % Allowed : 14.43 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.23), residues: 1260 helix: 0.80 (0.29), residues: 304 sheet: 0.22 (0.41), residues: 158 loop : -0.26 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.012 0.001 TYR D 76 PHE 0.024 0.001 PHE B 397 TRP 0.028 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (11700) covalent geometry : angle 0.46689 / 0.25 (16206) hydrogen bonds : bond 0.04040 / 2.88 ( 390) hydrogen bonds : angle 3.92264 / 2.83 ( 1007) metal coordination : bond 0.00813 / 0.49 ( 40) metal coordination : angle 2.48086 / 1.72 ( 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 233 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.368 Fit side-chains REVERT: A 65 GLN cc_start: 0.8457 (mt0) cc_final: 0.8065 (mt0) REVERT: B 10 ASP cc_start: 0.7798 (t0) cc_final: 0.7506 (t0) REVERT: B 222 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: B 294 ILE cc_start: 0.8327 (mt) cc_final: 0.7903 (tt) REVERT: B 393 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6243 (pp) REVERT: B 492 MET cc_start: 0.7403 (mmt) cc_final: 0.7174 (tpp) REVERT: E 126 ASP cc_start: 0.7664 (m-30) cc_final: 0.7447 (m-30) REVERT: E 334 ASN cc_start: 0.7074 (m110) cc_final: 0.6534 (m-40) REVERT: E 396 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7039 (ttt90) REVERT: E 441 PHE cc_start: 0.8396 (p90) cc_final: 0.8077 (p90) outliers start: 18 outliers final: 13 residues processed: 225 average time/residue: 0.4596 time to fit residues: 112.1073 Evaluate side-chains 228 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN D 10 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121625 restraints weight = 14306.755| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.78 r_work: 0.3483 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11740 Z= 0.157 Angle : 0.499 7.805 16239 Z= 0.258 Chirality : 0.040 0.154 1816 Planarity : 0.004 0.047 1862 Dihedral : 12.099 73.964 2314 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.47 % Allowed : 14.98 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1260 helix: 0.73 (0.29), residues: 304 sheet: 0.17 (0.41), residues: 158 loop : -0.31 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.014 0.001 TYR D 76 PHE 0.021 0.001 PHE B 397 TRP 0.035 0.001 TRP E 506 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (11700) covalent geometry : angle 0.48551 / 0.26 (16206) hydrogen bonds : bond 0.04236 / 3.02 ( 390) hydrogen bonds : angle 3.94660 / 2.84 ( 1007) metal coordination : bond 0.00929 / 0.56 ( 40) metal coordination : angle 2.62944 / 1.82 ( 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 230 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.240 Fit side-chains REVERT: A 65 GLN cc_start: 0.8479 (mt0) cc_final: 0.8091 (mt0) REVERT: B 222 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: B 294 ILE cc_start: 0.8335 (mt) cc_final: 0.7909 (tt) REVERT: B 393 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6240 (pp) REVERT: B 492 MET cc_start: 0.7413 (mmt) cc_final: 0.7193 (tpp) REVERT: E 126 ASP cc_start: 0.7672 (m-30) cc_final: 0.7458 (m-30) REVERT: E 334 ASN cc_start: 0.7091 (m110) cc_final: 0.6560 (m-40) REVERT: E 396 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7045 (ttt90) REVERT: E 441 PHE cc_start: 0.8413 (p90) cc_final: 0.8086 (p90) outliers start: 16 outliers final: 11 residues processed: 223 average time/residue: 0.4909 time to fit residues: 118.4578 Evaluate side-chains 230 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 28 optimal weight: 0.1980 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 126 optimal weight: 0.0170 chunk 32 optimal weight: 0.0060 chunk 6 optimal weight: 0.9980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN D 10 ASN B 272 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121857 restraints weight = 14415.946| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.64 r_work: 0.3490 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11740 Z= 0.105 Angle : 0.467 6.538 16239 Z= 0.244 Chirality : 0.039 0.153 1816 Planarity : 0.004 0.045 1862 Dihedral : 12.063 73.827 2314 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.47 % Allowed : 14.98 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1260 helix: 0.84 (0.29), residues: 306 sheet: 0.12 (0.41), residues: 158 loop : -0.25 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.011 0.001 TYR B 365 PHE 0.020 0.001 PHE B 397 TRP 0.031 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11700) covalent geometry : angle 0.45660 / 0.24 (16206) hydrogen bonds : bond 0.03851 / 2.74 ( 390) hydrogen bonds : angle 3.89422 / 2.81 ( 1007) metal coordination : bond 0.00605 / 0.37 ( 40) metal coordination : angle 2.17027 / 1.51 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.32 seconds wall clock time: 84 minutes 17.67 seconds (5057.67 seconds total)