Starting phenix.real_space_refine on Fri Feb 6 01:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q1j_72127/02_2026/9q1j_72127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q1j_72127/02_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_72127/02_2026/9q1j_72127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q1j_72127/02_2026/9q1j_72127.map" model { file = "/net/cci-nas-00/data/ceres_data/9q1j_72127/02_2026/9q1j_72127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q1j_72127/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 4.62, per 1000 atoms: 0.22 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: 1.66 Conformation dependent library (CDL) restraints added in 942.2 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: 2.47 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: 4.11 Time building geometry restraints manager: 2.15 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: 3.720 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 22.320 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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= 0.266 Angle : 0.747 6.851 30338 Z= 0.417 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 covalent geometry : bond 0.00469 (22078) covalent geometry : angle 0.74193 (30272) hydrogen bonds : bond 0.16007 ( 706) hydrogen bonds : angle 6.78806 ( 1934) metal coordination : bond 0.00544 ( 80) metal coordination : angle 1.96740 ( 66) Misc. bond : bond 0.05144 ( 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 : 0.671 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: 0.7060 time to fit residues: 238.6510 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 : 0.850 ------------------------------------------------------------------------------- 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: 5.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3760 r_free = 0.3760 target = 0.099340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064983 restraints weight = 43760.113| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.62 r_work: 0.2972 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22160 Z= 0.126 Angle : 0.524 6.833 30338 Z= 0.273 Chirality : 0.042 0.149 3362 Planarity : 0.004 0.047 3670 Dihedral : 10.759 73.851 3613 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.13 % Allowed : 9.99 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2548 helix: 0.29 (0.21), residues: 624 sheet: -0.55 (0.27), residues: 330 loop : 0.23 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 310 TYR 0.016 0.001 TYR C 96 PHE 0.016 0.001 PHE B 350 TRP 0.009 0.001 TRP B 385 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00285 (22078) covalent geometry : angle 0.51770 (30272) hydrogen bonds : bond 0.03776 ( 706) hydrogen bonds : angle 4.64832 ( 1934) metal coordination : bond 0.00632 ( 80) metal coordination : angle 1.79679 ( 66) Misc. bond : bond 0.00021 ( 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: 25 poor density : 179 time to evaluate : 0.758 Fit side-chains REVERT: A 122 MET cc_start: 0.8777 (mmt) cc_final: 0.8526 (mmm) REVERT: C 43 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8220 (tttp) REVERT: C 60 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 96 TYR cc_start: 0.8261 (m-80) cc_final: 0.7574 (m-80) REVERT: D 153 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: D 351 TYR cc_start: 0.7416 (m-80) cc_final: 0.6868 (m-80) REVERT: I 25 LYS cc_start: 0.8535 (tppt) cc_final: 0.8286 (ttpt) REVERT: I 43 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8275 (tttp) REVERT: I 60 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8142 (mm-30) REVERT: I 96 TYR cc_start: 0.8343 (m-80) cc_final: 0.7371 (m-80) REVERT: J 304 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8628 (mmtp) REVERT: J 351 TYR cc_start: 0.7368 (m-80) cc_final: 0.6739 (m-80) outliers start: 25 outliers final: 11 residues processed: 195 average time/residue: 0.5985 time to fit residues: 132.5703 Evaluate side-chains 166 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain H residue 483 VAL Chi-restraints excluded: chain I residue 49 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 90 optimal weight: 5.9990 chunk 141 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3747 r_free = 0.3747 target = 0.098420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063979 restraints weight = 44153.766| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.69 r_work: 0.2969 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1987 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= 0.128 Angle : 0.493 5.392 30338 Z= 0.256 Chirality : 0.042 0.145 3362 Planarity : 0.004 0.043 3670 Dihedral : 10.692 73.651 3613 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.08 % Allowed : 9.49 % Favored : 88.43 % 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: 0.17 (0.17), residues: 2548 helix: 0.50 (0.21), residues: 628 sheet: -0.67 (0.27), residues: 320 loop : 0.24 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 98 TYR 0.013 0.001 TYR H 447 PHE 0.016 0.001 PHE H 444 TRP 0.009 0.001 TRP J 227 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00301 (22078) covalent geometry : angle 0.48623 (30272) hydrogen bonds : bond 0.03364 ( 706) hydrogen bonds : angle 4.35411 ( 1934) metal coordination : bond 0.00872 ( 80) metal coordination : angle 1.81201 ( 66) Misc. bond : bond 0.00068 ( 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 211 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.720 Fit side-chains REVERT: A 122 MET cc_start: 0.8837 (mmt) cc_final: 0.8629 (mmm) REVERT: C 43 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8292 (tttp) REVERT: C 60 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8311 (mm-30) REVERT: C 96 TYR cc_start: 0.8300 (m-80) cc_final: 0.7582 (m-80) REVERT: D 351 TYR cc_start: 0.7391 (m-80) cc_final: 0.6943 (m-80) REVERT: I 43 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8280 (tttp) REVERT: I 60 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8268 (mm-30) REVERT: I 96 TYR cc_start: 0.8330 (m-80) cc_final: 0.7303 (m-80) REVERT: J 324 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8122 (p0) REVERT: J 326 PHE cc_start: 0.7986 (m-10) cc_final: 0.7742 (m-10) REVERT: J 351 TYR cc_start: 0.7268 (m-80) cc_final: 0.6593 (m-80) REVERT: J 377 PHE cc_start: 0.6666 (m-80) cc_final: 0.6365 (m-80) outliers start: 46 outliers final: 24 residues processed: 202 average time/residue: 0.5265 time to fit residues: 122.3724 Evaluate side-chains 177 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 61 LYS 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 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 169 MET Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 61 LYS 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 49 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 324 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 232 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3755 r_free = 0.3755 target = 0.098862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064521 restraints weight = 44203.439| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.69 r_work: 0.2962 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22160 Z= 0.096 Angle : 0.469 8.805 30338 Z= 0.240 Chirality : 0.041 0.149 3362 Planarity : 0.004 0.041 3670 Dihedral : 10.635 73.513 3613 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.81 % Allowed : 11.21 % Favored : 86.98 % 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: 0.33 (0.17), residues: 2548 helix: 0.70 (0.21), residues: 628 sheet: -0.64 (0.28), residues: 320 loop : 0.34 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 310 TYR 0.008 0.001 TYR G 76 PHE 0.020 0.001 PHE H 444 TRP 0.010 0.001 TRP J 348 HIS 0.003 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00223 (22078) covalent geometry : angle 0.46364 (30272) hydrogen bonds : bond 0.02918 ( 706) hydrogen bonds : angle 4.18826 ( 1934) metal coordination : bond 0.00555 ( 80) metal coordination : angle 1.63487 ( 66) Misc. bond : bond 0.00039 ( 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 205 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8162 (tttp) REVERT: C 60 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 96 TYR cc_start: 0.8143 (m-80) cc_final: 0.7472 (m-80) REVERT: D 153 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8052 (mmm) REVERT: D 351 TYR cc_start: 0.7307 (m-80) cc_final: 0.6864 (m-80) REVERT: D 474 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8058 (tt) REVERT: H 350 PHE cc_start: 0.7036 (m-80) cc_final: 0.6279 (m-80) REVERT: I 25 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8161 (ttmm) REVERT: I 43 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8162 (tttp) REVERT: I 60 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8200 (mm-30) REVERT: I 96 TYR cc_start: 0.8171 (m-80) cc_final: 0.7237 (m-80) REVERT: J 324 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8085 (p0) REVERT: J 351 TYR cc_start: 0.7162 (m-80) cc_final: 0.6391 (m-80) REVERT: J 377 PHE cc_start: 0.6628 (m-80) cc_final: 0.6355 (m-80) outliers start: 40 outliers final: 19 residues processed: 196 average time/residue: 0.4724 time to fit residues: 107.3904 Evaluate side-chains 172 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 MET Chi-restraints excluded: chain B residue 341 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 289 ARG Chi-restraints excluded: chain D residue 329 LEU 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 115 VAL Chi-restraints excluded: chain H residue 341 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 239 optimal weight: 4.9990 chunk 135 optimal weight: 0.0030 chunk 165 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 0.0040 chunk 8 optimal weight: 0.8980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.065271 restraints weight = 44179.137| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.68 r_work: 0.3003 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22160 Z= 0.087 Angle : 0.460 8.360 30338 Z= 0.236 Chirality : 0.040 0.161 3362 Planarity : 0.004 0.040 3670 Dihedral : 10.581 73.494 3613 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.76 % Allowed : 11.89 % Favored : 86.35 % 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: 0.41 (0.17), residues: 2548 helix: 0.80 (0.21), residues: 632 sheet: -0.65 (0.27), residues: 322 loop : 0.39 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 98 TYR 0.008 0.001 TYR A 76 PHE 0.026 0.001 PHE H 444 TRP 0.008 0.001 TRP D 348 HIS 0.003 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00195 (22078) covalent geometry : angle 0.45455 (30272) hydrogen bonds : bond 0.02756 ( 706) hydrogen bonds : angle 4.07142 ( 1934) metal coordination : bond 0.00532 ( 80) metal coordination : angle 1.57085 ( 66) Misc. bond : bond 0.00024 ( 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 201 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8127 (tttp) REVERT: C 60 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8252 (mm-30) REVERT: C 96 TYR cc_start: 0.7868 (m-80) cc_final: 0.7619 (m-80) REVERT: C 122 MET cc_start: 0.8830 (mtp) cc_final: 0.8592 (mtm) REVERT: D 153 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: D 351 TYR cc_start: 0.7317 (m-80) cc_final: 0.6866 (m-80) REVERT: D 474 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8040 (tt) REVERT: H 350 PHE cc_start: 0.7174 (m-80) cc_final: 0.6557 (m-80) REVERT: I 25 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: I 43 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8103 (tttp) REVERT: I 44 MET cc_start: 0.8083 (mmm) cc_final: 0.6800 (mtm) REVERT: I 60 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8135 (mm-30) REVERT: I 96 TYR cc_start: 0.8023 (m-80) cc_final: 0.7062 (m-80) REVERT: J 324 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8115 (p0) REVERT: J 351 TYR cc_start: 0.7213 (m-80) cc_final: 0.6395 (m-80) REVERT: J 377 PHE cc_start: 0.6604 (m-80) cc_final: 0.6319 (m-80) outliers start: 39 outliers final: 22 residues processed: 192 average time/residue: 0.5278 time to fit residues: 116.9981 Evaluate side-chains 179 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 VAL Chi-restraints excluded: chain B residue 341 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 127 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 329 LEU 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 290 VAL Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain I residue 25 LYS 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 Chi-restraints excluded: chain J residue 329 LEU 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: 2.9990 chunk 203 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3751 r_free = 0.3751 target = 0.098546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.064623 restraints weight = 44217.127| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.70 r_work: 0.2951 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22160 Z= 0.111 Angle : 0.475 11.536 30338 Z= 0.241 Chirality : 0.041 0.143 3362 Planarity : 0.004 0.041 3670 Dihedral : 10.578 73.509 3613 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.58 % Allowed : 12.75 % Favored : 85.67 % 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: 0.44 (0.17), residues: 2548 helix: 0.83 (0.21), residues: 626 sheet: -0.65 (0.27), residues: 322 loop : 0.41 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.013 0.001 TYR H 447 PHE 0.024 0.001 PHE D 326 TRP 0.007 0.001 TRP D 227 HIS 0.003 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00262 (22078) covalent geometry : angle 0.46851 (30272) hydrogen bonds : bond 0.02939 ( 706) hydrogen bonds : angle 4.07562 ( 1934) metal coordination : bond 0.00767 ( 80) metal coordination : angle 1.68722 ( 66) Misc. bond : bond 0.00045 ( 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 194 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6852 (m-80) cc_final: 0.6236 (m-80) REVERT: C 43 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8147 (tttp) REVERT: C 60 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 153 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8074 (mmm) REVERT: D 351 TYR cc_start: 0.7354 (m-80) cc_final: 0.6899 (m-80) REVERT: D 474 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8001 (tt) REVERT: D 491 TYR cc_start: 0.7882 (t80) cc_final: 0.7673 (t80) REVERT: H 350 PHE cc_start: 0.7195 (m-80) cc_final: 0.6785 (m-80) REVERT: I 25 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8219 (ttmt) REVERT: I 43 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8070 (tttp) REVERT: I 44 MET cc_start: 0.8061 (mmm) cc_final: 0.7806 (mmm) REVERT: I 60 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8123 (mm-30) REVERT: I 96 TYR cc_start: 0.8100 (m-80) cc_final: 0.7115 (m-80) REVERT: J 351 TYR cc_start: 0.7283 (m-80) cc_final: 0.6505 (m-80) REVERT: J 377 PHE cc_start: 0.6642 (m-80) cc_final: 0.6391 (m-80) outliers start: 35 outliers final: 29 residues processed: 186 average time/residue: 0.5138 time to fit residues: 110.5683 Evaluate side-chains 181 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 329 LEU 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 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 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 178 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 113 optimal weight: 0.0770 chunk 189 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3762 r_free = 0.3762 target = 0.099202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065418 restraints weight = 44210.885| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.72 r_work: 0.2993 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22160 Z= 0.090 Angle : 0.467 10.783 30338 Z= 0.238 Chirality : 0.040 0.151 3362 Planarity : 0.003 0.041 3670 Dihedral : 10.549 73.477 3613 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.81 % Allowed : 13.11 % Favored : 85.08 % 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: 0.50 (0.17), residues: 2548 helix: 0.92 (0.21), residues: 626 sheet: -0.64 (0.27), residues: 322 loop : 0.44 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.015 0.001 TYR C 96 PHE 0.014 0.001 PHE I 89 TRP 0.008 0.001 TRP D 227 HIS 0.003 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00208 (22078) covalent geometry : angle 0.46161 (30272) hydrogen bonds : bond 0.02749 ( 706) hydrogen bonds : angle 4.02578 ( 1934) metal coordination : bond 0.00574 ( 80) metal coordination : angle 1.58459 ( 66) Misc. bond : bond 0.00027 ( 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 191 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6875 (m-80) cc_final: 0.6355 (m-80) REVERT: C 43 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8183 (tttp) REVERT: C 44 MET cc_start: 0.8469 (mmp) cc_final: 0.8138 (mmm) REVERT: C 60 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 96 TYR cc_start: 0.7701 (m-80) cc_final: 0.6948 (m-80) REVERT: D 153 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: D 324 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7680 (p0) REVERT: D 351 TYR cc_start: 0.7278 (m-80) cc_final: 0.6815 (m-80) REVERT: D 474 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8021 (tt) REVERT: H 350 PHE cc_start: 0.7210 (m-80) cc_final: 0.6864 (m-80) REVERT: H 476 ARG cc_start: 0.6122 (pmt170) cc_final: 0.5815 (pmt170) REVERT: I 25 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8210 (ttmt) REVERT: I 43 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8022 (tttp) REVERT: I 44 MET cc_start: 0.8062 (mmm) cc_final: 0.7765 (mmm) REVERT: I 60 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8116 (mm-30) REVERT: I 96 TYR cc_start: 0.8090 (m-80) cc_final: 0.7152 (m-80) REVERT: J 153 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7982 (mmm) REVERT: J 351 TYR cc_start: 0.7197 (m-80) cc_final: 0.6355 (m-80) REVERT: J 377 PHE cc_start: 0.6591 (m-80) cc_final: 0.6285 (m-80) outliers start: 40 outliers final: 27 residues processed: 183 average time/residue: 0.5260 time to fit residues: 110.7719 Evaluate side-chains 180 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 329 LEU 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 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 153 MET Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 8 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 243 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3746 r_free = 0.3746 target = 0.098188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063975 restraints weight = 44127.945| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.69 r_work: 0.2953 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22160 Z= 0.120 Angle : 0.483 10.689 30338 Z= 0.247 Chirality : 0.041 0.154 3362 Planarity : 0.004 0.041 3670 Dihedral : 10.559 73.548 3613 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.54 % Allowed : 13.25 % Favored : 85.22 % 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: 0.39 (0.17), residues: 2548 helix: 0.80 (0.21), residues: 636 sheet: -0.65 (0.27), residues: 322 loop : 0.37 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.012 0.001 TYR H 447 PHE 0.013 0.001 PHE I 89 TRP 0.007 0.001 TRP J 227 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00284 (22078) covalent geometry : angle 0.47724 (30272) hydrogen bonds : bond 0.02987 ( 706) hydrogen bonds : angle 4.04915 ( 1934) metal coordination : bond 0.00896 ( 80) metal coordination : angle 1.70998 ( 66) Misc. bond : bond 0.00053 ( 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 186 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6891 (m-80) cc_final: 0.6316 (m-80) REVERT: B 476 ARG cc_start: 0.6093 (pmt170) cc_final: 0.5790 (pmt170) REVERT: C 43 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8157 (tttp) REVERT: C 60 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 96 TYR cc_start: 0.7842 (m-80) cc_final: 0.7506 (m-80) REVERT: D 153 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8081 (mmm) REVERT: D 315 MET cc_start: 0.8434 (tpt) cc_final: 0.8181 (tpp) REVERT: D 324 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7724 (p0) REVERT: D 351 TYR cc_start: 0.7301 (m-80) cc_final: 0.6828 (m-80) REVERT: D 474 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7990 (tt) REVERT: H 350 PHE cc_start: 0.7261 (m-80) cc_final: 0.6952 (m-80) REVERT: H 476 ARG cc_start: 0.6222 (pmt170) cc_final: 0.5884 (pmt170) REVERT: I 25 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8225 (ttmt) REVERT: I 43 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8083 (tttp) REVERT: I 44 MET cc_start: 0.8102 (mmm) cc_final: 0.7815 (mmm) REVERT: I 60 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8151 (mm-30) REVERT: I 96 TYR cc_start: 0.8205 (m-80) cc_final: 0.7307 (m-80) REVERT: J 153 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8011 (mmm) REVERT: J 351 TYR cc_start: 0.7219 (m-80) cc_final: 0.6402 (m-80) REVERT: J 377 PHE cc_start: 0.6555 (m-80) cc_final: 0.6317 (m-80) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.5659 time to fit residues: 117.7211 Evaluate side-chains 177 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 483 VAL 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 329 LEU 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 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 153 MET Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 210 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 137 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3762 r_free = 0.3762 target = 0.099214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.065322 restraints weight = 44294.759| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.61 r_work: 0.3006 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22160 Z= 0.087 Angle : 0.470 10.560 30338 Z= 0.239 Chirality : 0.041 0.145 3362 Planarity : 0.003 0.040 3670 Dihedral : 10.521 73.474 3613 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 13.52 % Favored : 84.95 % 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: 0.55 (0.17), residues: 2548 helix: 0.97 (0.21), residues: 628 sheet: -0.71 (0.28), residues: 310 loop : 0.49 (0.17), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.012 0.001 TYR C 96 PHE 0.018 0.001 PHE B 326 TRP 0.008 0.001 TRP J 227 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00200 (22078) covalent geometry : angle 0.46508 (30272) hydrogen bonds : bond 0.02694 ( 706) hydrogen bonds : angle 3.98621 ( 1934) metal coordination : bond 0.00526 ( 80) metal coordination : angle 1.59484 ( 66) Misc. bond : bond 0.00026 ( 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 183 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6840 (m-80) cc_final: 0.6254 (m-80) REVERT: B 476 ARG cc_start: 0.6058 (pmt170) cc_final: 0.5783 (pmt170) REVERT: C 43 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8215 (tttp) REVERT: C 44 MET cc_start: 0.8550 (mmp) cc_final: 0.8140 (mmm) REVERT: C 60 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 96 TYR cc_start: 0.7798 (m-80) cc_final: 0.7115 (m-80) REVERT: D 153 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8103 (mmm) REVERT: D 315 MET cc_start: 0.8477 (tpt) cc_final: 0.8188 (tpp) REVERT: D 324 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7744 (p0) REVERT: D 351 TYR cc_start: 0.7273 (m-80) cc_final: 0.6794 (m-80) REVERT: D 474 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7969 (tt) REVERT: H 350 PHE cc_start: 0.7239 (m-80) cc_final: 0.6922 (m-80) REVERT: H 476 ARG cc_start: 0.6178 (pmt170) cc_final: 0.5870 (pmt170) REVERT: I 43 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7945 (tttp) REVERT: I 96 TYR cc_start: 0.8229 (m-80) cc_final: 0.7400 (m-80) REVERT: J 351 TYR cc_start: 0.7251 (m-80) cc_final: 0.6430 (m-80) REVERT: J 377 PHE cc_start: 0.6623 (m-80) cc_final: 0.6350 (m-80) outliers start: 34 outliers final: 23 residues processed: 176 average time/residue: 0.5394 time to fit residues: 109.4839 Evaluate side-chains 167 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 MET 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 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 329 LEU 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 J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 222 optimal weight: 0.0010 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3746 r_free = 0.3746 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063944 restraints weight = 44207.658| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.70 r_work: 0.2949 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22160 Z= 0.124 Angle : 0.490 10.450 30338 Z= 0.248 Chirality : 0.041 0.161 3362 Planarity : 0.004 0.042 3670 Dihedral : 10.536 73.558 3613 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.42 (0.17), residues: 2548 helix: 0.78 (0.21), residues: 639 sheet: -0.52 (0.28), residues: 315 loop : 0.37 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.011 0.001 TYR B 447 PHE 0.011 0.001 PHE J 326 TRP 0.006 0.001 TRP J 227 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00293 (22078) covalent geometry : angle 0.48347 (30272) hydrogen bonds : bond 0.03048 ( 706) hydrogen bonds : angle 4.02938 ( 1934) metal coordination : bond 0.00866 ( 80) metal coordination : angle 1.71819 ( 66) Misc. bond : bond 0.00060 ( 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 177 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.6937 (m-80) cc_final: 0.6433 (m-80) REVERT: B 476 ARG cc_start: 0.6111 (pmt170) cc_final: 0.5777 (pmt170) REVERT: C 43 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8164 (tttp) REVERT: C 44 MET cc_start: 0.8549 (mmp) cc_final: 0.8033 (mmm) REVERT: C 60 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8147 (mm-30) REVERT: C 82 ASP cc_start: 0.8993 (p0) cc_final: 0.8786 (p0) REVERT: C 96 TYR cc_start: 0.7843 (m-80) cc_final: 0.7079 (m-80) REVERT: D 153 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8083 (mmm) REVERT: D 315 MET cc_start: 0.8496 (tpt) cc_final: 0.8276 (tpp) REVERT: D 324 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7765 (p0) REVERT: D 351 TYR cc_start: 0.7302 (m-80) cc_final: 0.6822 (m-80) REVERT: D 474 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7986 (tt) REVERT: H 350 PHE cc_start: 0.7309 (m-80) cc_final: 0.7039 (m-80) REVERT: H 476 ARG cc_start: 0.6213 (pmt170) cc_final: 0.5841 (pmt170) REVERT: I 43 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7940 (tttp) REVERT: I 60 GLU cc_start: 0.9037 (tp30) cc_final: 0.8597 (mm-30) REVERT: I 96 TYR cc_start: 0.8012 (m-80) cc_final: 0.7453 (m-80) REVERT: J 351 TYR cc_start: 0.7243 (m-80) cc_final: 0.6427 (m-80) outliers start: 29 outliers final: 23 residues processed: 172 average time/residue: 0.6092 time to fit residues: 120.6257 Evaluate side-chains 169 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 329 LEU 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 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 J residue 127 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 0.0570 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 255 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064255 restraints weight = 44210.051| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.70 r_work: 0.2957 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22160 Z= 0.108 Angle : 0.486 10.401 30338 Z= 0.247 Chirality : 0.041 0.149 3362 Planarity : 0.004 0.043 3670 Dihedral : 10.531 73.540 3613 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.27 % Allowed : 14.29 % Favored : 84.45 % 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: 0.47 (0.17), residues: 2548 helix: 0.86 (0.21), residues: 634 sheet: -0.53 (0.27), residues: 317 loop : 0.40 (0.17), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.011 0.001 TYR B 447 PHE 0.022 0.001 PHE B 326 TRP 0.007 0.001 TRP J 227 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00255 (22078) covalent geometry : angle 0.48044 (30272) hydrogen bonds : bond 0.02884 ( 706) hydrogen bonds : angle 4.01795 ( 1934) metal coordination : bond 0.00741 ( 80) metal coordination : angle 1.67579 ( 66) Misc. bond : bond 0.00043 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6319.89 seconds wall clock time: 108 minutes 33.74 seconds (6513.74 seconds total)