Starting phenix.real_space_refine on Fri Jul 3 02:08:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycl_72776/07_2026/9ycl_72776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycl_72776/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ycl_72776/07_2026/9ycl_72776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycl_72776/07_2026/9ycl_72776.map" model { file = "/net/cci-nas-00/data/ceres_data/9ycl_72776/07_2026/9ycl_72776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycl_72776/07_2026/9ycl_72776.cif" } 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-dev-6108/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: 2.89, per 1000 atoms: 0.26 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: 0.94 Conformation dependent library (CDL) restraints added in 392.0 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: 1.26 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: 2.09 Time building geometry restraints manager: 1.28 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: 15469 1.70 - 3.39: 647 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: 1732 0.114 - 0.227: 74 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: 4.670 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.990 Find NCS groups from input model: 0.190 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- 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= 0.306 Angle : 0.767 10.566 16239 Z= 0.498 Chirality : 0.058 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 0.00479 / 0.31 (11700) covalent geometry : angle 0.75264 / 0.50 (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 : 0.394 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: 0.6046 time to fit residues: 148.5888 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 : 0.377 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.4117 r_free = 0.4117 target = 0.161346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123423 restraints weight = 14603.358| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.90 r_work: 0.3486 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11740 Z= 0.115 Angle : 0.501 6.657 16239 Z= 0.261 Chirality : 0.040 0.202 1816 Planarity : 0.004 0.039 1862 Dihedral : 12.234 73.745 2314 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.92 % Allowed : 13.05 % Favored : 86.03 % 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 0.004 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 0.00257 / 0.11 (11700) covalent geometry : angle 0.48830 / 0.26 (16206) hydrogen bonds : bond 0.04776 / 3.37 ( 390) hydrogen bonds : angle 4.21323 / 3.03 ( 1007) metal coordination : bond 0.00710 / 0.50 ( 40) metal coordination : angle 2.51002 / 1.77 ( 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 : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8422 (m110) cc_final: 0.8113 (m-40) REVERT: A 65 GLN cc_start: 0.8317 (mt0) cc_final: 0.7967 (mt0) REVERT: D 25 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (tptp) REVERT: B 10 ASP cc_start: 0.7708 (t0) cc_final: 0.7451 (t0) REVERT: B 120 GLN cc_start: 0.8221 (mm110) cc_final: 0.7994 (mm110) REVERT: B 132 MET cc_start: 0.8173 (ttm) cc_final: 0.7910 (ttp) REVERT: B 294 ILE cc_start: 0.8314 (mt) cc_final: 0.7965 (tt) REVERT: B 492 MET cc_start: 0.7380 (mmt) cc_final: 0.7145 (mmp) REVERT: E 126 ASP cc_start: 0.7790 (m-30) cc_final: 0.7559 (m-30) REVERT: E 441 PHE cc_start: 0.8318 (p90) cc_final: 0.7954 (p90) outliers start: 10 outliers final: 3 residues processed: 232 average time/residue: 0.6055 time to fit residues: 151.4137 Evaluate side-chains 214 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 93 optimal weight: 0.0010 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 406 ASN B 515 ASN E 131 ASN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122615 restraints weight = 14677.049| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.75 r_work: 0.3493 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.003 0.030 11740 Z= 0.120 Angle : 0.482 6.253 16239 Z= 0.250 Chirality : 0.040 0.208 1816 Planarity : 0.004 0.045 1862 Dihedral : 12.125 73.726 2314 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.56 % Allowed : 12.96 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1260 helix: 0.60 (0.29), residues: 304 sheet: 0.25 (0.41), residues: 154 loop : -0.34 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.014 0.001 TYR B 365 PHE 0.011 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 0.00274 / 0.12 (11700) covalent geometry : angle 0.46956 / 0.25 (16206) hydrogen bonds : bond 0.04287 / 3.07 ( 390) hydrogen bonds : angle 3.97131 / 2.86 ( 1007) metal coordination : bond 0.00739 / 0.50 ( 40) metal coordination : angle 2.43138 / 1.71 ( 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 232 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8486 (m110) cc_final: 0.8201 (m-40) REVERT: A 40 ASN cc_start: 0.8338 (t0) cc_final: 0.8019 (t0) REVERT: A 65 GLN cc_start: 0.8360 (mt0) cc_final: 0.7984 (mt0) REVERT: B 10 ASP cc_start: 0.7700 (t0) cc_final: 0.7421 (t0) REVERT: B 294 ILE cc_start: 0.8316 (mt) cc_final: 0.7933 (tt) REVERT: B 393 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6267 (pp) REVERT: B 492 MET cc_start: 0.7395 (mmt) cc_final: 0.7146 (mmp) REVERT: E 126 ASP cc_start: 0.7730 (m-30) cc_final: 0.7501 (m-30) REVERT: E 441 PHE cc_start: 0.8354 (p90) cc_final: 0.7977 (p90) outliers start: 17 outliers final: 6 residues processed: 225 average time/residue: 0.5927 time to fit residues: 143.6605 Evaluate side-chains 218 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 103 CYS 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: 0.0770 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 130 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 406 ASN E 131 ASN E 246 GLN E 272 ASN E 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.160424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122894 restraints weight = 14617.082| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.72 r_work: 0.3486 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11740 Z= 0.130 Angle : 0.480 6.670 16239 Z= 0.249 Chirality : 0.040 0.155 1816 Planarity : 0.004 0.050 1862 Dihedral : 12.101 73.747 2314 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.75 % Allowed : 12.59 % Favored : 85.66 % 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: 0.70 (0.29), residues: 304 sheet: 0.29 (0.43), residues: 144 loop : -0.32 (0.22), residues: 812 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 0.013 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 0.00305 / 0.13 (11700) covalent geometry : angle 0.46742 / 0.25 (16206) hydrogen bonds : bond 0.04194 / 2.99 ( 390) hydrogen bonds : angle 3.93885 / 2.84 ( 1007) metal coordination : bond 0.00802 / 0.50 ( 40) metal coordination : angle 2.42145 / 1.67 ( 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 234 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8518 (m110) cc_final: 0.8232 (m-40) REVERT: A 65 GLN cc_start: 0.8395 (mt0) cc_final: 0.8048 (mt0) REVERT: A 91 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8195 (ptmm) REVERT: B 10 ASP cc_start: 0.7759 (t0) cc_final: 0.7494 (t0) REVERT: B 294 ILE cc_start: 0.8304 (mt) cc_final: 0.7921 (tt) REVERT: B 393 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6269 (pp) REVERT: B 492 MET cc_start: 0.7399 (mmt) cc_final: 0.7150 (mmp) REVERT: E 126 ASP cc_start: 0.7707 (m-30) cc_final: 0.7483 (m-30) REVERT: E 222 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: E 396 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7056 (ttt90) REVERT: E 441 PHE cc_start: 0.8350 (p90) cc_final: 0.7927 (p90) outliers start: 19 outliers final: 9 residues processed: 224 average time/residue: 0.6050 time to fit residues: 146.1037 Evaluate side-chains 225 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 91 LYS 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 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 Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 ASN B 42 ASN B 120 GLN B 406 ASN E 131 ASN E 246 GLN E 272 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120012 restraints weight = 14530.772| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.61 r_work: 0.3469 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11740 Z= 0.205 Angle : 0.536 8.848 16239 Z= 0.275 Chirality : 0.042 0.156 1816 Planarity : 0.005 0.052 1862 Dihedral : 12.163 74.001 2314 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 12.87 % Favored : 84.83 % 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: -0.27 (0.23), residues: 1260 helix: 0.38 (0.28), residues: 316 sheet: 0.06 (0.41), residues: 160 loop : -0.42 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.017 0.002 TYR D 76 PHE 0.012 0.002 PHE B 73 TRP 0.018 0.001 TRP E 506 HIS 0.006 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.20 (11700) covalent geometry : angle 0.51818 / 0.27 (16206) hydrogen bonds : bond 0.04767 / 3.39 ( 390) hydrogen bonds : angle 4.03482 / 2.90 ( 1007) metal coordination : bond 0.01241 / 0.75 ( 40) metal coordination : angle 3.06534 / 2.08 ( 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 238 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.338 Fit side-chains REVERT: A 65 GLN cc_start: 0.8509 (mt0) cc_final: 0.8257 (mt0) REVERT: B 10 ASP cc_start: 0.7776 (t0) cc_final: 0.7473 (t0) REVERT: B 222 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: B 294 ILE cc_start: 0.8334 (mt) cc_final: 0.7929 (tt) REVERT: B 393 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6381 (pp) REVERT: B 492 MET cc_start: 0.7406 (mmt) cc_final: 0.7149 (mmt) REVERT: E 126 ASP cc_start: 0.7679 (m-30) cc_final: 0.7449 (m-30) REVERT: E 396 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7097 (ttt90) REVERT: E 441 PHE cc_start: 0.8368 (p90) cc_final: 0.8078 (p90) outliers start: 25 outliers final: 10 residues processed: 226 average time/residue: 0.5952 time to fit residues: 145.0639 Evaluate side-chains 225 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 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 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 396 ARG Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4096 r_free = 0.4096 target = 0.159686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121680 restraints weight = 14519.766| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.65 r_work: 0.3481 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11740 Z= 0.145 Angle : 0.496 7.909 16239 Z= 0.256 Chirality : 0.040 0.189 1816 Planarity : 0.004 0.051 1862 Dihedral : 12.113 73.793 2314 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.84 % Allowed : 13.88 % 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: -0.23 (0.23), residues: 1260 helix: 0.43 (0.29), residues: 316 sheet: 0.13 (0.41), residues: 158 loop : -0.41 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.013 0.001 TYR B 365 PHE 0.015 0.001 PHE B 397 TRP 0.016 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11700) covalent geometry : angle 0.47875 / 0.26 (16206) hydrogen bonds : bond 0.04232 / 3.02 ( 390) hydrogen bonds : angle 3.95111 / 2.84 ( 1007) metal coordination : bond 0.00864 / 0.53 ( 40) metal coordination : angle 2.90985 / 2.06 ( 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 232 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.362 Fit side-chains REVERT: A 65 GLN cc_start: 0.8485 (mt0) cc_final: 0.8228 (mt0) REVERT: B 10 ASP cc_start: 0.7776 (t0) cc_final: 0.7479 (t0) REVERT: B 222 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: B 294 ILE cc_start: 0.8330 (mt) cc_final: 0.7922 (tt) REVERT: B 393 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6331 (pp) REVERT: B 492 MET cc_start: 0.7441 (mmt) cc_final: 0.7176 (mmt) REVERT: E 126 ASP cc_start: 0.7668 (m-30) cc_final: 0.7442 (m-30) REVERT: E 396 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7043 (ttt90) REVERT: E 441 PHE cc_start: 0.8348 (p90) cc_final: 0.8019 (p90) REVERT: E 498 VAL cc_start: 0.7739 (t) cc_final: 0.7414 (p) REVERT: E 503 PHE cc_start: 0.8801 (m-80) cc_final: 0.8563 (m-80) outliers start: 20 outliers final: 12 residues processed: 222 average time/residue: 0.5702 time to fit residues: 136.3429 Evaluate side-chains 224 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 396 ARG Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 114 optimal weight: 0.0020 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 11 optimal weight: 0.0020 chunk 127 optimal weight: 1.9990 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN D 10 ASN 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 = 0.4113 r_free = 0.4113 target = 0.161120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122382 restraints weight = 14456.738| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.61 r_work: 0.3504 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11740 Z= 0.091 Angle : 0.449 6.276 16239 Z= 0.235 Chirality : 0.039 0.165 1816 Planarity : 0.004 0.044 1862 Dihedral : 12.046 73.674 2314 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 0.13 (0.23), residues: 1260 helix: 0.86 (0.30), residues: 306 sheet: 0.22 (0.41), residues: 158 loop : -0.19 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 310 TYR 0.013 0.001 TYR B 365 PHE 0.016 0.001 PHE B 397 TRP 0.020 0.001 TRP E 506 HIS 0.004 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (11700) covalent geometry : angle 0.43992 / 0.23 (16206) hydrogen bonds : bond 0.03618 / 2.58 ( 390) hydrogen bonds : angle 3.82314 / 2.75 ( 1007) metal coordination : bond 0.00470 / 0.29 ( 40) metal coordination : angle 2.05292 / 1.44 ( 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 235 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.283 Fit side-chains REVERT: A 32 ASN cc_start: 0.8522 (m110) cc_final: 0.8242 (m-40) REVERT: A 65 GLN cc_start: 0.8404 (mt0) cc_final: 0.8006 (mt0) REVERT: B 10 ASP cc_start: 0.7776 (t0) cc_final: 0.7484 (t0) REVERT: B 222 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: B 294 ILE cc_start: 0.8300 (mt) cc_final: 0.7907 (tt) REVERT: B 393 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6244 (pp) REVERT: B 492 MET cc_start: 0.7429 (mmt) cc_final: 0.7193 (tpp) REVERT: E 126 ASP cc_start: 0.7671 (m-30) cc_final: 0.7451 (m-30) REVERT: E 441 PHE cc_start: 0.8346 (p90) cc_final: 0.7994 (p90) REVERT: E 503 PHE cc_start: 0.8796 (m-80) cc_final: 0.8557 (m-80) outliers start: 17 outliers final: 11 residues processed: 225 average time/residue: 0.5100 time to fit residues: 123.8184 Evaluate side-chains 230 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 87 SER 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 145 GLN 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 132 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 20 optimal weight: 0.0770 chunk 126 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN D 10 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 = 0.4102 r_free = 0.4102 target = 0.160172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121831 restraints weight = 14369.851| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.76 r_work: 0.3481 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11740 Z= 0.146 Angle : 0.486 7.664 16239 Z= 0.251 Chirality : 0.040 0.184 1816 Planarity : 0.004 0.047 1862 Dihedral : 12.080 73.835 2314 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 14.43 % Favored : 83.82 % 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: 0.80 (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 0.005 0.000 ARG B 314 TYR 0.013 0.001 TYR D 76 PHE 0.009 0.001 PHE E 73 TRP 0.025 0.001 TRP E 506 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11700) covalent geometry : angle 0.47259 / 0.25 (16206) hydrogen bonds : bond 0.04079 / 2.91 ( 390) hydrogen bonds : angle 3.89532 / 2.81 ( 1007) metal coordination : bond 0.00841 / 0.51 ( 40) metal coordination : angle 2.57590 / 1.78 ( 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 232 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.369 Fit side-chains REVERT: A 65 GLN cc_start: 0.8454 (mt0) cc_final: 0.8072 (mt0) REVERT: B 10 ASP cc_start: 0.7759 (t0) cc_final: 0.7466 (t0) REVERT: B 222 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: B 294 ILE cc_start: 0.8315 (mt) cc_final: 0.7908 (tt) REVERT: B 393 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6258 (pp) REVERT: B 492 MET cc_start: 0.7429 (mmt) cc_final: 0.7204 (tpp) REVERT: E 126 ASP cc_start: 0.7684 (m-30) cc_final: 0.7461 (m-30) REVERT: E 396 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7018 (ttt90) REVERT: E 441 PHE cc_start: 0.8384 (p90) cc_final: 0.8055 (p90) REVERT: E 503 PHE cc_start: 0.8796 (m-80) cc_final: 0.8568 (m-80) outliers start: 19 outliers final: 13 residues processed: 224 average time/residue: 0.5012 time to fit residues: 121.3966 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 103 CYS 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 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 41 VAL Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.0570 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4101 r_free = 0.4101 target = 0.160025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121099 restraints weight = 14338.292| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.61 r_work: 0.3484 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.034 11740 Z= 0.146 Angle : 0.491 7.773 16239 Z= 0.254 Chirality : 0.040 0.282 1816 Planarity : 0.004 0.046 1862 Dihedral : 12.086 73.824 2314 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 14.43 % Favored : 83.64 % 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: 0.76 (0.29), residues: 304 sheet: 0.23 (0.41), residues: 158 loop : -0.25 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.013 0.001 TYR D 76 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 0.00350 / 0.15 (11700) covalent geometry : angle 0.47727 / 0.25 (16206) hydrogen bonds : bond 0.04090 / 2.91 ( 390) hydrogen bonds : angle 3.93738 / 2.84 ( 1007) metal coordination : bond 0.00840 / 0.49 ( 40) metal coordination : angle 2.56796 / 1.76 ( 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 230 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.411 Fit side-chains REVERT: A 65 GLN cc_start: 0.8472 (mt0) cc_final: 0.8090 (mt0) REVERT: A 91 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8241 (ptmm) REVERT: B 10 ASP cc_start: 0.7741 (t0) cc_final: 0.7460 (t0) REVERT: B 222 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: B 294 ILE cc_start: 0.8330 (mt) cc_final: 0.7916 (tt) REVERT: B 393 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6280 (pp) REVERT: B 406 ASN cc_start: 0.7737 (t0) cc_final: 0.7534 (t0) REVERT: B 492 MET cc_start: 0.7401 (mmt) cc_final: 0.7182 (tpp) REVERT: E 126 ASP cc_start: 0.7671 (m-30) cc_final: 0.7452 (m-30) REVERT: E 334 ASN cc_start: 0.6812 (m110) cc_final: 0.6444 (m-40) REVERT: E 396 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7013 (ttt90) REVERT: E 441 PHE cc_start: 0.8387 (p90) cc_final: 0.8064 (p90) REVERT: E 503 PHE cc_start: 0.8782 (m-80) cc_final: 0.8491 (m-80) outliers start: 21 outliers final: 13 residues processed: 221 average time/residue: 0.5540 time to fit residues: 132.0623 Evaluate side-chains 224 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 103 CYS 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 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 396 ARG Chi-restraints excluded: chain E residue 419 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN 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 = 0.4096 r_free = 0.4096 target = 0.159615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120609 restraints weight = 14320.005| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.62 r_work: 0.3477 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11740 Z= 0.167 Angle : 0.506 8.376 16239 Z= 0.262 Chirality : 0.041 0.352 1816 Planarity : 0.004 0.047 1862 Dihedral : 12.102 73.893 2314 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.65 % Allowed : 14.61 % Favored : 83.73 % 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: 0.67 (0.29), residues: 304 sheet: 0.24 (0.41), residues: 158 loop : -0.30 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.015 0.001 TYR D 76 PHE 0.015 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 0.00402 / 0.17 (11700) covalent geometry : angle 0.49143 / 0.26 (16206) hydrogen bonds : bond 0.04333 / 3.08 ( 390) hydrogen bonds : angle 3.98066 / 2.87 ( 1007) metal coordination : bond 0.00965 / 0.57 ( 40) metal coordination : angle 2.74752 / 1.89 ( 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 224 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.379 Fit side-chains REVERT: A 65 GLN cc_start: 0.8486 (mt0) cc_final: 0.8226 (mt0) REVERT: A 91 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8238 (ptmm) REVERT: B 222 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: B 294 ILE cc_start: 0.8346 (mt) cc_final: 0.7921 (tt) REVERT: B 393 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6297 (pp) REVERT: B 406 ASN cc_start: 0.7768 (t0) cc_final: 0.7534 (t0) REVERT: B 492 MET cc_start: 0.7401 (mmt) cc_final: 0.7191 (tpp) REVERT: E 126 ASP cc_start: 0.7672 (m-30) cc_final: 0.7449 (m-30) REVERT: E 334 ASN cc_start: 0.6822 (m110) cc_final: 0.6430 (m110) REVERT: E 396 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7034 (ttt90) REVERT: E 441 PHE cc_start: 0.8402 (p90) cc_final: 0.8134 (p90) outliers start: 18 outliers final: 13 residues processed: 218 average time/residue: 0.4857 time to fit residues: 114.4270 Evaluate side-chains 224 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 91 LYS 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 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 396 ARG Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 419 LYS 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: 0.8980 chunk 28 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 6 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN 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 = 0.4097 r_free = 0.4097 target = 0.159737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121588 restraints weight = 14411.373| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.85 r_work: 0.3476 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11740 Z= 0.150 Angle : 0.498 8.027 16239 Z= 0.258 Chirality : 0.041 0.290 1816 Planarity : 0.004 0.047 1862 Dihedral : 12.095 73.827 2314 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.84 % Allowed : 14.52 % Favored : 83.64 % 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: -0.01 (0.23), residues: 1260 helix: 0.71 (0.29), residues: 304 sheet: 0.22 (0.41), residues: 158 loop : -0.29 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.013 0.001 TYR D 76 PHE 0.017 0.001 PHE B 397 TRP 0.034 0.001 TRP E 506 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11700) covalent geometry : angle 0.48385 / 0.26 (16206) hydrogen bonds : bond 0.04188 / 2.98 ( 390) hydrogen bonds : angle 3.97356 / 2.86 ( 1007) metal coordination : bond 0.00858 / 0.51 ( 40) metal coordination : angle 2.63269 / 1.81 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.02 seconds wall clock time: 95 minutes 49.42 seconds (5749.42 seconds total)