Starting phenix.real_space_refine on Sat Jul 4 16:04:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.map" model { file = "/net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q1j_72127/07_2026/9q1j_72127.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 20 6.06 5 P 56 5.49 5 Mg 4 5.21 5 S 208 5.16 5 C 13422 2.51 5 N 3630 2.21 5 O 4070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21410 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "C" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "D" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "E" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 472 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "F" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "G" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "H" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "I" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "J" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 472 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "L" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} 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: "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: "C" 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: 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: "G" 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: "H" 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: "I" 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: "J" 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 520 SG CYS A 74 27.596 97.190 63.718 1.00 28.65 S ATOM 546 SG CYS A 77 30.556 97.077 66.202 1.00 27.34 S ATOM 651 SG CYS A 90 29.796 100.293 64.380 1.00 35.97 S ATOM 854 SG CYS A 117 17.061 113.553 55.911 1.00 98.27 S ATOM 874 SG CYS A 120 16.276 114.814 59.344 1.00 92.35 S ATOM 935 SG CYS A 128 13.695 112.792 57.541 1.00103.39 S ATOM 947 SG CYS A 130 14.338 116.306 56.372 1.00120.32 S ATOM 2577 SG CYS B 207 31.226 76.582 38.902 1.00 43.90 S ATOM 2597 SG CYS B 210 29.935 73.617 36.843 1.00 45.16 S ATOM 2718 SG CYS B 226 32.430 72.990 39.685 1.00 50.65 S ATOM 3018 SG CYS B 261 43.190 50.264 61.384 1.00 37.52 S ATOM 3148 SG CYS B 279 40.116 52.467 60.333 1.00 37.91 S ATOM 4538 SG CYS B 452 35.050 31.732 11.881 1.00155.83 S ATOM 4652 SG CYS B 477 38.618 32.780 12.953 1.00145.21 S ATOM 4694 SG CYS B 484 36.178 35.380 11.468 1.00138.00 S ATOM 5560 SG CYS C 74 53.492 114.748 101.060 1.00 50.40 S ATOM 5586 SG CYS C 77 56.043 112.089 102.155 1.00 49.27 S ATOM 5691 SG CYS C 90 55.741 115.335 104.147 1.00 61.04 S ATOM 5894 SG CYS C 117 44.079 129.686 111.819 1.00128.61 S ATOM 5914 SG CYS C 120 42.958 129.796 115.478 1.00153.25 S ATOM 5975 SG CYS C 128 40.883 127.875 112.951 1.00134.23 S ATOM 5987 SG CYS C 130 40.835 131.542 112.919 1.00152.49 S ATOM 7617 SG CYS D 207 58.884 126.466 71.268 1.00 35.75 S ATOM 7637 SG CYS D 210 57.723 126.819 67.676 1.00 59.46 S ATOM 7758 SG CYS D 226 60.131 124.010 68.550 1.00 44.58 S ATOM 8058 SG CYS D 261 68.603 93.378 58.887 1.00 35.83 S ATOM 8188 SG CYS D 279 65.778 95.657 60.353 1.00 41.77 S ATOM 9578 SG CYS D 452 62.834 128.752 21.800 1.00157.93 S ATOM 9692 SG CYS D 477 65.748 128.280 19.270 1.00150.81 S ATOM 9734 SG CYS D 484 65.793 131.156 21.853 1.00137.92 S ATOM 11213 SG CYS G 74 100.117 49.803 63.719 1.00 28.65 S ATOM 11239 SG CYS G 77 97.160 49.925 66.206 1.00 27.34 S ATOM 11344 SG CYS G 90 97.909 46.706 64.385 1.00 35.97 S ATOM 11547 SG CYS G 117 110.600 33.408 55.909 1.00 98.27 S ATOM 11567 SG CYS G 120 111.386 32.147 59.342 1.00 92.35 S ATOM 11628 SG CYS G 128 113.970 34.161 57.535 1.00103.39 S ATOM 11640 SG CYS G 130 113.317 30.648 56.369 1.00120.32 S ATOM 13270 SG CYS H 207 96.516 70.408 38.896 1.00 43.90 S ATOM 13290 SG CYS H 210 97.812 73.368 36.834 1.00 45.16 S ATOM 13411 SG CYS H 226 95.322 74.003 39.678 1.00 50.65 S ATOM 13711 SG CYS H 261 84.645 96.769 61.376 1.00 37.52 S ATOM 13841 SG CYS H 279 87.712 94.557 60.323 1.00 37.91 S ATOM 15231 SG CYS H 452 92.782 115.254 11.855 1.00155.83 S ATOM 15345 SG CYS H 477 89.212 114.216 12.931 1.00145.21 S ATOM 15387 SG CYS H 484 91.644 111.608 11.445 1.00138.00 S ATOM 16253 SG CYS I 74 74.214 32.333 101.097 1.00 50.40 S ATOM 16279 SG CYS I 77 71.671 35.000 102.193 1.00 49.27 S ATOM 16384 SG CYS I 90 71.966 31.754 104.187 1.00 61.04 S ATOM 16587 SG CYS I 117 83.598 17.376 111.854 1.00128.61 S ATOM 16607 SG CYS I 120 84.723 17.265 115.512 1.00153.25 S ATOM 16668 SG CYS I 128 86.800 19.179 112.982 1.00134.23 S ATOM 16680 SG CYS I 130 86.839 15.512 112.952 1.00152.49 S ATOM 18310 SG CYS J 207 68.759 20.614 71.317 1.00 35.75 S ATOM 18330 SG CYS J 210 69.916 20.256 67.724 1.00 59.46 S ATOM 18451 SG CYS J 226 67.516 23.072 68.599 1.00 44.58 S ATOM 18751 SG CYS J 261 59.115 53.721 58.929 1.00 35.83 S ATOM 18881 SG CYS J 279 61.936 51.436 60.393 1.00 41.77 S ATOM 20271 SG CYS J 452 64.752 18.313 21.854 1.00157.93 S ATOM 20385 SG CYS J 477 61.836 18.791 19.327 1.00150.81 S ATOM 20427 SG CYS J 484 61.786 15.917 21.912 1.00137.92 S Time building chain proxies: 4.51, per 1000 atoms: 0.21 Number of scatterers: 21410 At special positions: 0 Unit cell: (128.635, 147.886, 131.26, 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 20 29.99 S 208 16.00 P 56 15.00 Mg 4 11.99 O 4070 8.00 N 3630 7.00 C 13422 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 814.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 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 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 477 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 77 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 74 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 130 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 128 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 120 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 117 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 229 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 210 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 207 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 226 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" NE2 HIS D 257 " pdb="ZN ZN D 603 " - pdb=" ND1 HIS D 264 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 279 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 261 " pdb=" ZN D 604 " pdb="ZN ZN D 604 " - pdb=" ND1 HIS D 487 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 484 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 452 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 477 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 77 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 74 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 128 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 120 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 117 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 130 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" ND1 HIS H 229 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 210 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 226 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 207 " pdb=" ZN H 603 " pdb="ZN ZN H 603 " - pdb=" ND1 HIS H 264 " pdb="ZN ZN H 603 " - pdb=" NE2 HIS H 257 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 261 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 279 " pdb=" ZN H 604 " pdb="ZN ZN H 604 " - pdb=" ND1 HIS H 487 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 452 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 484 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 477 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 77 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 90 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 74 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 130 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 120 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 117 " pdb=" ZN J 602 " pdb="ZN ZN J 602 " - pdb=" ND1 HIS J 229 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 210 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 207 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 226 " pdb=" ZN J 603 " pdb="ZN ZN J 603 " - pdb=" NE2 HIS J 257 " pdb="ZN ZN J 603 " - pdb=" ND1 HIS J 264 " pdb="ZN ZN J 603 " - pdb=" SG CYS J 279 " pdb="ZN ZN J 603 " - pdb=" SG CYS J 261 " pdb=" ZN J 604 " pdb="ZN ZN J 604 " - pdb=" ND1 HIS J 487 " pdb="ZN ZN J 604 " - pdb=" SG CYS J 484 " pdb="ZN ZN J 604 " - pdb=" SG CYS J 452 " pdb="ZN ZN J 604 " - pdb=" SG CYS J 477 " Number of angles added : 66 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4808 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 36 sheets defined 29.8% alpha, 17.1% beta 26 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 2.44 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 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 106 through 114 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.791A pdb=" N ARG B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 143 through 155 removed outlier: 4.651A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.580A pdb=" N LYS B 155 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.823A pdb=" N ILE B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.883A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.517A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.528A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.738A pdb=" N SER B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 378 removed outlier: 3.911A pdb=" N THR B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.641A pdb=" N ALA B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 436 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 437' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 484 through 504 removed outlier: 3.742A pdb=" N ARG B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.725A pdb=" N PHE C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.506A pdb=" N CYS C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 74 through 80 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 143 through 155 removed outlier: 4.865A pdb=" N HIS D 148 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 158 through 175 removed outlier: 3.551A pdb=" N ILE D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 removed outlier: 4.136A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 removed outlier: 3.648A pdb=" N GLY D 248 " --> pdb=" O GLN D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 301 through 324 removed outlier: 3.542A pdb=" N LEU D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 removed outlier: 3.772A pdb=" N VAL D 437 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 504 removed outlier: 3.874A pdb=" N ARG D 492 " --> pdb=" O ALA D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 10 through 18 Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.792A pdb=" N ARG H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 143 through 155 removed outlier: 4.608A pdb=" N HIS H 148 " --> pdb=" O GLN H 145 " (cutoff:3.500A) Proline residue: H 151 - end of helix removed outlier: 3.580A pdb=" N LYS H 155 " --> pdb=" O LEU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 175 removed outlier: 3.823A pdb=" N ILE H 164 " --> pdb=" O ASN H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 196 removed outlier: 3.883A pdb=" N ALA H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 removed outlier: 3.517A pdb=" N GLY H 248 " --> pdb=" O GLN H 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 245 through 248' Processing helix chain 'H' and resid 252 through 258 Processing helix chain 'H' and resid 269 through 287 removed outlier: 3.528A pdb=" N VAL H 287 " --> pdb=" O HIS H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 325 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.738A pdb=" N SER H 374 " --> pdb=" O TYR H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 378 removed outlier: 3.910A pdb=" N THR H 378 " --> pdb=" O ASP H 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 375 through 378' Processing helix chain 'H' and resid 432 through 437 removed outlier: 3.641A pdb=" N ALA H 435 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 436 " --> pdb=" O LYS H 433 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL H 437 " --> pdb=" O SER H 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 432 through 437' Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 484 through 504 removed outlier: 3.741A pdb=" N ARG H 492 " --> pdb=" O ALA H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 521 Processing helix chain 'I' and resid 7 through 9 No H-bonds generated for 'chain 'I' and resid 7 through 9' Processing helix chain 'I' and resid 10 through 20 removed outlier: 3.725A pdb=" N PHE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 33 Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.505A pdb=" N CYS I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 74' Processing helix chain 'I' and resid 74 through 80 Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'J' and resid 75 through 82 Processing helix chain 'J' and resid 143 through 155 removed outlier: 4.878A pdb=" N HIS J 148 " --> pdb=" O GLN J 145 " (cutoff:3.500A) Proline residue: J 151 - end of helix Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.551A pdb=" N ILE J 164 " --> pdb=" O ASN J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 196 removed outlier: 4.135A pdb=" N ALA J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 248 removed outlier: 3.648A pdb=" N GLY J 248 " --> pdb=" O GLN J 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 245 through 248' Processing helix chain 'J' and resid 252 through 258 Processing helix chain 'J' and resid 269 through 287 Processing helix chain 'J' and resid 301 through 324 removed outlier: 3.541A pdb=" N LEU J 322 " --> pdb=" O LYS J 318 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP J 324 " --> pdb=" O ALA J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 437 removed outlier: 3.773A pdb=" N VAL J 437 " --> pdb=" O SER J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 484 through 504 removed outlier: 3.874A pdb=" N ARG J 492 " --> pdb=" O ALA J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.741A pdb=" N TYR 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: 6.649A pdb=" N GLU B 92 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU B 109 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 90 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 111 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 88 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.649A pdb=" N GLU B 92 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU B 109 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 90 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 111 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 88 " --> pdb=" O PHE B 111 " (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 364 through 365 removed outlier: 9.620A pdb=" N GLU B 364 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE B 350 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 351 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 328 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 383 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS B 330 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TRP B 385 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.505A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 7 through 10 removed outlier: 3.850A pdb=" N LYS D 9 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR D 124 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N MET D 57 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 12.375A pdb=" N THR D 122 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 118 removed outlier: 6.636A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 109 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP D 90 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 111 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY D 88 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 118 removed outlier: 6.636A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 109 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP D 90 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 111 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY D 88 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 200 removed outlier: 3.709A pdb=" N THR D 223 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 364 through 365 removed outlier: 3.908A pdb=" N VAL D 381 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP D 385 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.374A pdb=" N TYR D 446 " --> pdb=" O ILE D 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AC3, first strand: chain 'H' and resid 53 through 55 removed outlier: 4.741A pdb=" N TYR H 124 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 116 through 118 removed outlier: 6.649A pdb=" N GLU H 92 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU H 109 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP H 90 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE H 111 " --> pdb=" O GLY H 88 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY H 88 " --> pdb=" O PHE H 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 116 through 118 removed outlier: 6.649A pdb=" N GLU H 92 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU H 109 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP H 90 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE H 111 " --> pdb=" O GLY H 88 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY H 88 " --> pdb=" O PHE H 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'H' and resid 364 through 365 removed outlier: 9.620A pdb=" N GLU H 364 " --> pdb=" O TRP H 348 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE H 350 " --> pdb=" O GLU H 364 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 351 " --> pdb=" O ASP H 331 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL H 328 " --> pdb=" O VAL H 381 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU H 383 " --> pdb=" O VAL H 328 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS H 330 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TRP H 385 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS H 382 " --> pdb=" O ILE H 397 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS H 399 " --> pdb=" O CYS H 382 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE H 384 " --> pdb=" O CYS H 399 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE H 401 " --> pdb=" O PHE H 384 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER H 396 " --> pdb=" O TYR H 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AC9, first strand: chain 'H' and resid 446 through 447 removed outlier: 6.506A pdb=" N TYR H 446 " --> pdb=" O ILE H 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD2, first strand: chain 'J' and resid 7 through 10 removed outlier: 3.850A pdb=" N LYS J 9 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR J 124 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N MET J 57 " --> pdb=" O THR J 122 " (cutoff:3.500A) removed outlier: 12.375A pdb=" N THR J 122 " --> pdb=" O MET J 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 34 through 35 Processing sheet with id=AD4, first strand: chain 'J' and resid 116 through 118 removed outlier: 6.637A pdb=" N GLU J 92 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU J 109 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP J 90 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE J 111 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY J 88 " --> pdb=" O PHE J 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 116 through 118 removed outlier: 6.637A pdb=" N GLU J 92 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU J 109 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP J 90 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE J 111 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY J 88 " --> pdb=" O PHE J 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 199 through 200 removed outlier: 3.708A pdb=" N THR J 223 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 364 through 365 removed outlier: 3.907A pdb=" N VAL J 381 " --> pdb=" O VAL J 328 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP J 385 " --> pdb=" O ILE J 332 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 410 through 412 Processing sheet with id=AD9, first strand: chain 'J' and resid 446 through 447 removed outlier: 6.374A pdb=" N TYR J 446 " --> pdb=" O ILE J 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 662 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3300 1.28 - 1.41: 6100 1.41 - 1.55: 12265 1.55 - 1.68: 141 1.68 - 1.81: 272 Bond restraints: 22078 Sorted by residual: bond pdb=" C12 F86 E 39 " pdb=" N2 F86 E 39 " ideal model delta sigma weight residual 1.293 1.353 -0.060 1.00e-02 1.00e+04 3.59e+01 bond pdb=" C12 F86 K 39 " pdb=" N2 F86 K 39 " ideal model delta sigma weight residual 1.293 1.353 -0.060 1.00e-02 1.00e+04 3.55e+01 bond pdb=" N VAL D 328 " pdb=" CA VAL D 328 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.25e-02 6.40e+03 7.70e+00 bond pdb=" N VAL J 328 " pdb=" CA VAL J 328 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.25e-02 6.40e+03 7.25e+00 bond pdb=" N HIS J 188 " pdb=" CA HIS J 188 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.82e+00 ... (remaining 22073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 28548 1.37 - 2.74: 1361 2.74 - 4.11: 227 4.11 - 5.48: 76 5.48 - 6.85: 60 Bond angle restraints: 30272 Sorted by residual: angle pdb=" N GLU H 99 " pdb=" CA GLU H 99 " pdb=" C GLU H 99 " ideal model delta sigma weight residual 114.56 110.02 4.54 1.27e+00 6.20e-01 1.28e+01 angle pdb=" N GLU B 99 " pdb=" CA GLU B 99 " pdb=" C GLU B 99 " ideal model delta sigma weight residual 114.56 110.03 4.53 1.27e+00 6.20e-01 1.27e+01 angle pdb=" C9 F86 E 39 " pdb=" C11 F86 E 39 " pdb=" N5 F86 E 39 " ideal model delta sigma weight residual 120.19 123.73 -3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" C9 F86 K 39 " pdb=" C11 F86 K 39 " pdb=" N5 F86 K 39 " ideal model delta sigma weight residual 120.19 123.71 -3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" C THR B 97 " pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 ... (remaining 30267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12040 17.90 - 35.79: 708 35.79 - 53.69: 143 53.69 - 71.59: 85 71.59 - 89.48: 22 Dihedral angle restraints: 12998 sinusoidal: 5510 harmonic: 7488 Sorted by residual: dihedral pdb=" CA VAL D 287 " pdb=" C VAL D 287 " pdb=" N LYS D 288 " pdb=" CA LYS D 288 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL J 287 " pdb=" C VAL J 287 " pdb=" N LYS J 288 " pdb=" CA LYS J 288 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA THR B 97 " pdb=" C THR B 97 " pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 12995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3154 0.115 - 0.229: 154 0.229 - 0.344: 0 0.344 - 0.458: 26 0.458 - 0.573: 28 Chirality restraints: 3362 Sorted by residual: chirality pdb=" P A K 31 " pdb=" OP1 A K 31 " pdb=" OP2 A K 31 " pdb=" O5' A K 31 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" P G K 1 " pdb=" OP1 G K 1 " pdb=" OP2 G K 1 " pdb=" O5' G K 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.17e+00 chirality pdb=" P G E 1 " pdb=" OP1 G E 1 " pdb=" OP2 G E 1 " pdb=" O5' G E 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.14e+00 ... (remaining 3359 not shown) Planarity restraints: 3670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J 19 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO J 20 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO J 20 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 20 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 19 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO D 20 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 144 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ASP D 144 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP D 144 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN D 145 " 0.011 2.00e-02 2.50e+03 ... (remaining 3667 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1542 2.74 - 3.28: 20001 3.28 - 3.82: 35540 3.82 - 4.36: 44940 4.36 - 4.90: 74290 Nonbonded interactions: 176313 Sorted by model distance: nonbonded pdb=" OP1 C L 6 " pdb="MG MG J 601 " model vdw 2.200 2.170 nonbonded pdb=" OP1 C F 6 " pdb="MG MG D 601 " model vdw 2.200 2.170 nonbonded pdb=" O PRO B 203 " pdb=" OH TYR B 237 " model vdw 2.235 3.040 nonbonded pdb=" O PRO H 203 " pdb=" OH TYR H 237 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN I 85 " pdb=" O PHE I 89 " model vdw 2.306 3.120 ... (remaining 176308 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 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.620 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 0.060 22160 Z= 0.273 Angle : 0.747 6.851 30338 Z= 0.427 Chirality : 0.079 0.573 3362 Planarity : 0.005 0.053 3670 Dihedral : 13.439 89.483 8190 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -0.29 (0.16), residues: 2548 helix: -0.47 (0.20), residues: 616 sheet: -0.60 (0.27), residues: 342 loop : 0.15 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.010 0.001 TYR G 76 PHE 0.018 0.002 PHE C 68 TRP 0.012 0.001 TRP J 227 HIS 0.006 0.001 HIS H 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.27 (22078) covalent geometry : angle 0.74192 / 0.43 (30272) hydrogen bonds : bond 0.16007 / 10.62 ( 706) hydrogen bonds : angle 6.78806 / 4.67 ( 1934) metal coordination : bond 0.00544 / 0.36 ( 80) metal coordination : angle 1.96740 / 1.35 ( 66) Misc. bond : bond 0.05144 / 2.58 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7810 (mm-30) REVERT: C 89 PHE cc_start: 0.7925 (m-10) cc_final: 0.7697 (m-80) REVERT: D 351 TYR cc_start: 0.7232 (m-80) cc_final: 0.6559 (m-80) REVERT: I 44 MET cc_start: 0.8705 (mmm) cc_final: 0.8488 (mmp) REVERT: I 89 PHE cc_start: 0.8009 (m-10) cc_final: 0.7678 (m-80) REVERT: J 351 TYR cc_start: 0.7147 (m-80) cc_final: 0.6920 (m-80) outliers start: 0 outliers final: 1 residues processed: 304 average time/residue: 0.7351 time to fit residues: 249.3310 Evaluate side-chains 158 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 169 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 ASN D 145 GLN J 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.099464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.065203 restraints weight = 43744.617| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.62 r_work: 0.2975 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22160 Z= 0.132 Angle : 0.538 8.042 30338 Z= 0.285 Chirality : 0.043 0.150 3362 Planarity : 0.004 0.054 3670 Dihedral : 10.804 73.697 3613 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % 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 (0.17), residues: 2548 helix: 0.20 (0.20), residues: 622 sheet: -0.55 (0.27), residues: 330 loop : 0.20 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 310 TYR 0.018 0.001 TYR C 96 PHE 0.017 0.001 PHE H 326 TRP 0.009 0.001 TRP H 385 HIS 0.006 0.001 HIS H 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (22078) covalent geometry : angle 0.53039 / 0.28 (30272) hydrogen bonds : bond 0.04106 / 2.73 ( 706) hydrogen bonds : angle 4.84903 / 3.37 ( 1934) metal coordination : bond 0.00923 / 0.61 ( 80) metal coordination : angle 1.99020 / 1.41 ( 66) Misc. bond : bond 0.00075 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.631 Fit side-chains REVERT: C 43 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8223 (tttp) REVERT: C 60 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 96 TYR cc_start: 0.8235 (m-80) cc_final: 0.7489 (m-80) REVERT: D 153 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: D 351 TYR cc_start: 0.7416 (m-80) cc_final: 0.6886 (m-80) REVERT: I 25 LYS cc_start: 0.8511 (tppt) cc_final: 0.8245 (ttpt) REVERT: I 43 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8232 (tttp) REVERT: I 60 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8133 (mm-30) REVERT: I 96 TYR cc_start: 0.8277 (m-80) cc_final: 0.7313 (m-80) REVERT: J 324 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8175 (p0) REVERT: J 351 TYR cc_start: 0.7354 (m-80) cc_final: 0.6695 (m-80) outliers start: 28 outliers final: 11 residues processed: 194 average time/residue: 0.5911 time to fit residues: 131.1086 Evaluate side-chains 163 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 324 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 90 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 9 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 254 optimal weight: 50.0000 chunk 148 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN B 410 ASN C 85 ASN G 85 ASN H 410 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.098207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063724 restraints weight = 44045.296| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.69 r_work: 0.2940 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22160 Z= 0.146 Angle : 0.504 6.752 30338 Z= 0.266 Chirality : 0.043 0.147 3362 Planarity : 0.004 0.047 3670 Dihedral : 10.713 73.547 3613 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.31 % Allowed : 9.58 % Favored : 88.11 % 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: 0.16 (0.17), residues: 2548 helix: 0.50 (0.21), residues: 624 sheet: -0.64 (0.27), residues: 330 loop : 0.24 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 98 TYR 0.019 0.001 TYR H 447 PHE 0.018 0.001 PHE C 89 TRP 0.010 0.001 TRP D 348 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22078) covalent geometry : angle 0.49740 / 0.27 (30272) hydrogen bonds : bond 0.03718 / 2.47 ( 706) hydrogen bonds : angle 4.52131 / 3.15 ( 1934) metal coordination : bond 0.00797 / 0.52 ( 80) metal coordination : angle 1.75155 / 1.23 ( 66) Misc. bond : bond 0.00379 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.827 Fit side-chains REVERT: A 122 MET cc_start: 0.8847 (mmt) cc_final: 0.8643 (mmm) REVERT: C 43 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8106 (tttp) REVERT: C 60 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8190 (mm-30) REVERT: C 96 TYR cc_start: 0.8247 (m-80) cc_final: 0.7509 (m-80) REVERT: D 58 MET cc_start: 0.8826 (mtp) cc_final: 0.8569 (mtp) REVERT: D 153 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: D 324 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (p0) REVERT: D 351 TYR cc_start: 0.7366 (m-80) cc_final: 0.6873 (m-80) REVERT: G 11 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8370 (p) REVERT: I 43 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8196 (tttp) REVERT: I 60 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8184 (mm-30) REVERT: I 96 TYR cc_start: 0.8265 (m-80) cc_final: 0.7243 (m-80) REVERT: J 304 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8768 (mmtp) REVERT: J 351 TYR cc_start: 0.7220 (m-80) cc_final: 0.6589 (m-80) REVERT: J 377 PHE cc_start: 0.6574 (m-80) cc_final: 0.6338 (m-80) outliers start: 51 outliers final: 23 residues processed: 213 average time/residue: 0.5520 time to fit residues: 135.7083 Evaluate side-chains 182 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 304 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 48 optimal weight: 0.7980 chunk 79 optimal weight: 0.0020 chunk 232 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN C 85 ASN D 314 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.065124 restraints weight = 44155.943| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.65 r_work: 0.2975 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 22160 Z= 0.090 Angle : 0.477 8.953 30338 Z= 0.247 Chirality : 0.041 0.170 3362 Planarity : 0.004 0.042 3670 Dihedral : 10.669 73.530 3613 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.40 % Allowed : 11.44 % Favored : 87.16 % 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: 0.26 (0.17), residues: 2548 helix: 0.70 (0.21), residues: 628 sheet: -0.65 (0.28), residues: 320 loop : 0.26 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 476 TYR 0.011 0.001 TYR H 447 PHE 0.018 0.001 PHE H 444 TRP 0.013 0.001 TRP D 348 HIS 0.003 0.001 HIS H 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (22078) covalent geometry : angle 0.47023 / 0.25 (30272) hydrogen bonds : bond 0.03092 / 2.04 ( 706) hydrogen bonds : angle 4.33229 / 3.02 ( 1934) metal coordination : bond 0.00411 / 0.27 ( 80) metal coordination : angle 1.78378 / 1.26 ( 66) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.807 Fit side-chains REVERT: A 11 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 43 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8305 (tttp) REVERT: C 60 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 96 TYR cc_start: 0.8260 (m-80) cc_final: 0.7305 (m-80) REVERT: D 315 MET cc_start: 0.8647 (tpp) cc_final: 0.8442 (tpp) REVERT: D 324 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8528 (p0) REVERT: D 351 TYR cc_start: 0.7356 (m-80) cc_final: 0.6870 (m-80) REVERT: D 474 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8055 (tt) REVERT: I 43 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8212 (tttp) REVERT: I 60 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8245 (mm-30) REVERT: I 96 TYR cc_start: 0.8225 (m-80) cc_final: 0.7183 (m-80) REVERT: J 351 TYR cc_start: 0.7205 (m-80) cc_final: 0.6490 (m-80) REVERT: J 377 PHE cc_start: 0.6691 (m-80) cc_final: 0.6397 (m-80) REVERT: J 474 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8225 (tt) outliers start: 31 outliers final: 19 residues processed: 193 average time/residue: 0.5549 time to fit residues: 123.5879 Evaluate side-chains 176 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 chunk 135 optimal weight: 0.0370 chunk 165 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN D 314 HIS G 85 ASN J 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063991 restraints weight = 44137.715| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.68 r_work: 0.2949 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22160 Z= 0.125 Angle : 0.479 8.128 30338 Z= 0.249 Chirality : 0.042 0.153 3362 Planarity : 0.004 0.040 3670 Dihedral : 10.635 73.587 3613 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.12 % Allowed : 11.62 % Favored : 86.26 % 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 (0.17), residues: 2548 helix: 0.72 (0.21), residues: 628 sheet: -0.67 (0.28), residues: 322 loop : 0.27 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 310 TYR 0.010 0.001 TYR A 76 PHE 0.027 0.001 PHE H 444 TRP 0.013 0.001 TRP D 348 HIS 0.004 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (22078) covalent geometry : angle 0.47351 / 0.25 (30272) hydrogen bonds : bond 0.03221 / 2.15 ( 706) hydrogen bonds : angle 4.26938 / 2.98 ( 1934) metal coordination : bond 0.00658 / 0.42 ( 80) metal coordination : angle 1.67708 / 1.19 ( 66) Misc. bond : bond 0.00029 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 43 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8169 (tttp) REVERT: C 60 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8231 (mm-30) REVERT: C 96 TYR cc_start: 0.8164 (m-80) cc_final: 0.7215 (m-80) REVERT: D 153 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: D 351 TYR cc_start: 0.7338 (m-80) cc_final: 0.6868 (m-80) REVERT: D 474 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8036 (tt) REVERT: H 350 PHE cc_start: 0.7040 (m-80) cc_final: 0.6317 (m-80) REVERT: I 43 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8135 (tttp) REVERT: I 60 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8201 (mm-30) REVERT: I 96 TYR cc_start: 0.8093 (m-80) cc_final: 0.7091 (m-80) REVERT: J 351 TYR cc_start: 0.7193 (m-80) cc_final: 0.6409 (m-80) REVERT: J 377 PHE cc_start: 0.6603 (m-80) cc_final: 0.6380 (m-80) REVERT: J 474 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8216 (tt) outliers start: 47 outliers final: 27 residues processed: 200 average time/residue: 0.5761 time to fit residues: 133.5588 Evaluate side-chains 184 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 474 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 114 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN D 314 HIS G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064179 restraints weight = 44134.824| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.69 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22160 Z= 0.110 Angle : 0.480 11.319 30338 Z= 0.247 Chirality : 0.041 0.157 3362 Planarity : 0.003 0.040 3670 Dihedral : 10.636 73.555 3613 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.63 % Allowed : 12.48 % Favored : 85.90 % 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: 0.28 (0.17), residues: 2548 helix: 0.71 (0.21), residues: 628 sheet: -0.68 (0.28), residues: 322 loop : 0.29 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 310 TYR 0.015 0.001 TYR C 96 PHE 0.019 0.001 PHE H 444 TRP 0.008 0.001 TRP D 227 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (22078) covalent geometry : angle 0.47411 / 0.25 (30272) hydrogen bonds : bond 0.03100 / 2.06 ( 706) hydrogen bonds : angle 4.21150 / 2.94 ( 1934) metal coordination : bond 0.00579 / 0.36 ( 80) metal coordination : angle 1.73409 / 1.22 ( 66) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.845 Fit side-chains REVERT: A 11 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8399 (p) REVERT: C 43 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8190 (tttp) REVERT: C 60 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8252 (mm-30) REVERT: C 96 TYR cc_start: 0.8033 (m-80) cc_final: 0.7355 (m-80) REVERT: D 153 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8121 (mmm) REVERT: D 349 LYS cc_start: 0.8875 (tppp) cc_final: 0.8564 (tppt) REVERT: D 351 TYR cc_start: 0.7332 (m-80) cc_final: 0.6781 (m-80) REVERT: D 474 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8053 (tt) REVERT: H 350 PHE cc_start: 0.7036 (m-80) cc_final: 0.6417 (m-80) REVERT: I 43 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8106 (tttp) REVERT: I 44 MET cc_start: 0.8174 (mmm) cc_final: 0.6991 (mtm) REVERT: I 60 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8217 (mm-30) REVERT: I 96 TYR cc_start: 0.8013 (m-80) cc_final: 0.6949 (m-80) REVERT: J 351 TYR cc_start: 0.7225 (m-80) cc_final: 0.6457 (m-80) REVERT: J 377 PHE cc_start: 0.6688 (m-80) cc_final: 0.6435 (m-80) REVERT: J 474 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (tt) outliers start: 36 outliers final: 25 residues processed: 190 average time/residue: 0.6016 time to fit residues: 131.8829 Evaluate side-chains 182 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 474 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 23 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 171 optimal weight: 0.0980 chunk 216 optimal weight: 9.9990 chunk 113 optimal weight: 0.0470 chunk 189 optimal weight: 8.9990 chunk 133 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN D 314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065487 restraints weight = 44011.774| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.64 r_work: 0.2986 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22160 Z= 0.086 Angle : 0.476 12.200 30338 Z= 0.244 Chirality : 0.041 0.178 3362 Planarity : 0.003 0.041 3670 Dihedral : 10.613 73.501 3613 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.40 % Allowed : 12.84 % Favored : 85.76 % 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: 0.35 (0.17), residues: 2548 helix: 0.78 (0.20), residues: 632 sheet: -0.64 (0.28), residues: 322 loop : 0.33 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 476 TYR 0.010 0.001 TYR C 96 PHE 0.038 0.001 PHE D 326 TRP 0.008 0.001 TRP D 227 HIS 0.006 0.000 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (22078) covalent geometry : angle 0.46936 / 0.24 (30272) hydrogen bonds : bond 0.02853 / 1.90 ( 706) hydrogen bonds : angle 4.13325 / 2.89 ( 1934) metal coordination : bond 0.00327 / 0.22 ( 80) metal coordination : angle 1.79828 / 1.23 ( 66) Misc. bond : bond 0.00003 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 476 ARG cc_start: 0.6693 (ptp90) cc_final: 0.6249 (pmt170) REVERT: C 43 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8165 (tttp) REVERT: C 60 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8267 (mm-30) REVERT: C 96 TYR cc_start: 0.7984 (m-80) cc_final: 0.7465 (m-80) REVERT: C 122 MET cc_start: 0.8749 (mtp) cc_final: 0.8524 (mtm) REVERT: D 153 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: D 349 LYS cc_start: 0.8850 (tppp) cc_final: 0.8547 (tppt) REVERT: D 351 TYR cc_start: 0.7360 (m-80) cc_final: 0.6664 (m-80) REVERT: D 474 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8011 (tt) REVERT: H 350 PHE cc_start: 0.7068 (m-80) cc_final: 0.6462 (m-80) REVERT: I 43 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8080 (tttp) REVERT: I 44 MET cc_start: 0.8129 (mmm) cc_final: 0.7168 (mtm) REVERT: I 60 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8212 (mm-30) REVERT: I 96 TYR cc_start: 0.8005 (m-80) cc_final: 0.7023 (m-80) REVERT: J 351 TYR cc_start: 0.7255 (m-80) cc_final: 0.6471 (m-80) REVERT: J 377 PHE cc_start: 0.6749 (m-80) cc_final: 0.6487 (m-80) REVERT: J 474 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8215 (tt) outliers start: 31 outliers final: 22 residues processed: 186 average time/residue: 0.5862 time to fit residues: 126.2095 Evaluate side-chains 178 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 474 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 8 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN D 314 HIS G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.096325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061855 restraints weight = 43960.164| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.67 r_work: 0.2903 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22160 Z= 0.244 Angle : 0.600 29.722 30338 Z= 0.294 Chirality : 0.045 0.199 3362 Planarity : 0.004 0.040 3670 Dihedral : 10.669 73.895 3610 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.99 % Allowed : 13.02 % Favored : 84.99 % 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: 0.02 (0.17), residues: 2548 helix: 0.44 (0.20), residues: 628 sheet: -0.76 (0.27), residues: 332 loop : 0.13 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 476 TYR 0.014 0.001 TYR G 76 PHE 0.019 0.002 PHE B 326 TRP 0.009 0.001 TRP D 86 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (22078) covalent geometry : angle 0.55172 / 0.29 (30272) hydrogen bonds : bond 0.04053 / 2.73 ( 706) hydrogen bonds : angle 4.36321 / 3.05 ( 1934) metal coordination : bond 0.01639 / 1.00 ( 80) metal coordination : angle 5.08284 / 3.54 ( 66) Misc. bond : bond 0.00120 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6899 (m-80) cc_final: 0.6189 (m-80) REVERT: C 43 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8311 (tttp) REVERT: C 60 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8300 (mm-30) REVERT: C 96 TYR cc_start: 0.8248 (m-80) cc_final: 0.7696 (m-80) REVERT: D 153 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8203 (mmm) REVERT: D 324 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7725 (p0) REVERT: D 349 LYS cc_start: 0.8884 (tppp) cc_final: 0.8588 (tptp) REVERT: D 351 TYR cc_start: 0.7469 (m-80) cc_final: 0.7018 (m-80) REVERT: D 474 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8079 (tt) REVERT: H 350 PHE cc_start: 0.7090 (m-80) cc_final: 0.6866 (m-80) REVERT: I 43 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8237 (tttp) REVERT: I 44 MET cc_start: 0.8318 (mmm) cc_final: 0.7039 (mtm) REVERT: I 60 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8221 (mm-30) REVERT: I 96 TYR cc_start: 0.8349 (m-80) cc_final: 0.7298 (m-80) REVERT: J 315 MET cc_start: 0.8491 (tpp) cc_final: 0.8206 (tpp) REVERT: J 351 TYR cc_start: 0.7433 (m-80) cc_final: 0.6638 (m-80) REVERT: J 377 PHE cc_start: 0.6907 (m-80) cc_final: 0.6464 (m-80) REVERT: J 474 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (tt) outliers start: 44 outliers final: 28 residues processed: 191 average time/residue: 0.5950 time to fit residues: 131.3184 Evaluate side-chains 180 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 210 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 0.0030 chunk 65 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN D 314 HIS G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063918 restraints weight = 43501.738| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.67 r_work: 0.2948 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22160 Z= 0.101 Angle : 0.517 19.866 30338 Z= 0.256 Chirality : 0.041 0.155 3362 Planarity : 0.003 0.039 3670 Dihedral : 10.651 73.600 3610 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.27 % Allowed : 14.24 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2548 helix: 0.61 (0.21), residues: 624 sheet: -0.76 (0.28), residues: 322 loop : 0.24 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 476 TYR 0.008 0.001 TYR J 154 PHE 0.019 0.001 PHE H 326 TRP 0.010 0.001 TRP D 227 HIS 0.005 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (22078) covalent geometry : angle 0.48613 / 0.25 (30272) hydrogen bonds : bond 0.03105 / 2.07 ( 706) hydrogen bonds : angle 4.20224 / 2.94 ( 1934) metal coordination : bond 0.00819 / 0.53 ( 80) metal coordination : angle 3.81561 / 2.67 ( 66) Misc. bond : bond 0.00001 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6807 (m-80) cc_final: 0.6049 (m-80) REVERT: C 43 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8190 (tttp) REVERT: C 60 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8202 (mm-30) REVERT: C 96 TYR cc_start: 0.8015 (m-80) cc_final: 0.7580 (m-80) REVERT: D 153 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8096 (mmm) REVERT: D 324 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7704 (p0) REVERT: D 349 LYS cc_start: 0.8864 (tppp) cc_final: 0.8572 (tppt) REVERT: D 351 TYR cc_start: 0.7405 (m-80) cc_final: 0.6779 (m-80) REVERT: D 474 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8030 (tt) REVERT: H 350 PHE cc_start: 0.7119 (m-80) cc_final: 0.6743 (m-80) REVERT: I 43 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8073 (tttp) REVERT: I 44 MET cc_start: 0.8024 (mmm) cc_final: 0.6924 (mtm) REVERT: I 60 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8122 (mm-30) REVERT: I 96 TYR cc_start: 0.8179 (m-80) cc_final: 0.7169 (m-80) REVERT: J 351 TYR cc_start: 0.7314 (m-80) cc_final: 0.6574 (m-80) REVERT: J 377 PHE cc_start: 0.6832 (m-80) cc_final: 0.6569 (m-80) outliers start: 28 outliers final: 23 residues processed: 177 average time/residue: 0.5868 time to fit residues: 120.5122 Evaluate side-chains 173 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 222 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 94 optimal weight: 0.0470 chunk 33 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 overall best weight: 0.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN G 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064379 restraints weight = 43378.191| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.67 r_work: 0.2961 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22160 Z= 0.095 Angle : 0.500 14.745 30338 Z= 0.249 Chirality : 0.041 0.241 3362 Planarity : 0.004 0.042 3670 Dihedral : 10.564 73.543 3610 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.31 % Allowed : 14.10 % Favored : 84.58 % 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: 0.26 (0.17), residues: 2548 helix: 0.67 (0.21), residues: 628 sheet: -0.73 (0.28), residues: 322 loop : 0.30 (0.17), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 476 TYR 0.014 0.001 TYR H 447 PHE 0.026 0.001 PHE B 326 TRP 0.009 0.001 TRP J 520 HIS 0.004 0.001 HIS H 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22078) covalent geometry : angle 0.47572 / 0.25 (30272) hydrogen bonds : bond 0.02978 / 1.99 ( 706) hydrogen bonds : angle 4.11591 / 2.88 ( 1934) metal coordination : bond 0.00593 / 0.39 ( 80) metal coordination : angle 3.30352 / 2.42 ( 66) Misc. bond : bond 0.00026 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8405 (p) REVERT: B 350 PHE cc_start: 0.6841 (m-80) cc_final: 0.6121 (m-80) REVERT: C 43 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8163 (tttp) REVERT: C 60 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8195 (mm-30) REVERT: C 96 TYR cc_start: 0.7912 (m-80) cc_final: 0.7694 (m-80) REVERT: D 153 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8063 (mmm) REVERT: D 324 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7682 (p0) REVERT: D 349 LYS cc_start: 0.8856 (tppp) cc_final: 0.8541 (tptp) REVERT: D 351 TYR cc_start: 0.7410 (m-80) cc_final: 0.6906 (m-80) REVERT: D 474 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (tt) REVERT: H 350 PHE cc_start: 0.7128 (m-80) cc_final: 0.6773 (m-80) REVERT: I 25 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8189 (ttmt) REVERT: I 43 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8050 (tttp) REVERT: I 44 MET cc_start: 0.8024 (mmm) cc_final: 0.6944 (mtm) REVERT: I 60 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8109 (mm-30) REVERT: I 96 TYR cc_start: 0.8144 (m-80) cc_final: 0.7134 (m-80) REVERT: J 324 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8037 (p0) REVERT: J 351 TYR cc_start: 0.7322 (m-80) cc_final: 0.6583 (m-80) REVERT: J 377 PHE cc_start: 0.6738 (m-80) cc_final: 0.6493 (m-80) outliers start: 29 outliers final: 23 residues processed: 175 average time/residue: 0.5706 time to fit residues: 116.0304 Evaluate side-chains 173 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 324 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064188 restraints weight = 43443.754| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.67 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22160 Z= 0.108 Angle : 0.498 12.916 30338 Z= 0.251 Chirality : 0.042 0.174 3362 Planarity : 0.004 0.044 3670 Dihedral : 10.551 73.547 3610 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 13.92 % Favored : 84.54 % 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 (0.17), residues: 2548 helix: 0.70 (0.21), residues: 632 sheet: -0.73 (0.28), residues: 322 loop : 0.29 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 476 TYR 0.013 0.001 TYR H 447 PHE 0.026 0.001 PHE H 326 TRP 0.009 0.001 TRP J 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (22078) covalent geometry : angle 0.47863 / 0.25 (30272) hydrogen bonds : bond 0.03029 / 2.03 ( 706) hydrogen bonds : angle 4.09749 / 2.87 ( 1934) metal coordination : bond 0.00646 / 0.41 ( 80) metal coordination : angle 2.98059 / 2.16 ( 66) Misc. bond : bond 0.00040 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6994.81 seconds wall clock time: 120 minutes 25.44 seconds (7225.44 seconds total)