Starting phenix.real_space_refine on Tue Apr 7 15:28:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j9e_61266/04_2026/9j9e_61266.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians Zn 13 6.06 5 P 91 5.49 5 S 118 5.16 5 C 17575 2.51 5 N 4910 2.21 5 O 5684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28391 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1113 Classifications: {'RNA': 53} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 25, 'rna3p': 27} Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 829 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 35} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1902 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 7, 'TRANS': 231} Chain: "D1" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1533 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D2" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1542 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "D3" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1542 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "D4" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1542 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "D5" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1533 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D6" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1533 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D7" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1533 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D8" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1322 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain breaks: 2 Chain: "E1" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1399 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 1 Chain: "E2" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4897 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 581} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E3" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1399 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 1 Chain: "E4" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4759 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 563} Chain breaks: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E2" 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: "E4" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2497 SG CYS C 70 31.609 119.719 36.858 1.00113.35 S ATOM 2617 SG CYS C 85 34.730 119.766 34.314 1.00114.22 S ATOM 2636 SG CYS C 88 35.374 121.908 37.180 1.00115.47 S ATOM 4382 SG CYSD1 71 56.037 76.104 43.778 1.00 81.22 S ATOM 4456 SG CYSD1 81 55.104 73.134 41.250 1.00 82.84 S ATOM 4477 SG CYSD1 84 52.999 73.898 44.252 1.00 80.25 S ATOM 4497 SG CYSD1 87 53.203 76.577 41.764 1.00 78.19 S ATOM 5924 SG CYSD2 71 75.551 90.117 67.547 1.00 51.48 S ATOM 5998 SG CYSD2 81 77.437 87.599 65.154 1.00 52.49 S ATOM 6019 SG CYSD2 84 75.411 86.371 68.123 1.00 50.67 S ATOM 6039 SG CYSD2 87 73.517 88.113 65.565 1.00 47.80 S ATOM 7466 SG CYSD3 71 75.312 114.455 92.377 1.00 37.28 S ATOM 7540 SG CYSD3 81 78.520 114.635 90.180 1.00 38.49 S ATOM 7561 SG CYSD3 84 78.221 112.085 92.985 1.00 37.13 S ATOM 7581 SG CYSD3 87 75.812 111.652 90.356 1.00 34.09 S ATOM 9008 SG CYSD4 71 55.030 127.562 117.450 1.00 33.91 S ATOM 9082 SG CYSD4 81 56.807 130.209 115.306 1.00 31.32 S ATOM 9103 SG CYSD4 84 58.739 128.557 118.096 1.00 31.91 S ATOM 9123 SG CYSD4 87 57.610 126.314 115.401 1.00 30.78 S ATOM 10541 SG CYSD5 71 31.818 117.585 141.525 1.00 37.56 S ATOM 10615 SG CYSD5 81 30.803 120.777 139.566 1.00 36.72 S ATOM 10636 SG CYSD5 84 33.175 121.097 142.463 1.00 35.87 S ATOM 10656 SG CYSD5 87 34.338 119.125 139.597 1.00 33.27 S ATOM 12074 SG CYSD6 71 25.446 92.445 164.276 1.00 40.62 S ATOM 12148 SG CYSD6 81 22.337 93.492 162.282 1.00 39.71 S ATOM 12169 SG CYSD6 84 23.457 95.549 165.276 1.00 37.35 S ATOM 12189 SG CYSD6 87 25.834 95.438 162.513 1.00 35.65 S ATOM 13607 SG CYSD7 71 42.104 71.095 186.414 1.00118.52 S ATOM 13681 SG CYSD7 81 39.232 69.403 184.191 1.00115.88 S ATOM 13702 SG CYSD7 84 38.355 71.304 187.268 1.00115.73 S ATOM 13722 SG CYSD7 87 39.915 73.315 184.751 1.00115.34 S ATOM 15076 SG CYSD8 71 68.242 70.858 209.807 1.00193.06 S ATOM 15150 SG CYSD8 81 67.831 67.677 207.384 1.00192.55 S ATOM 15171 SG CYSD8 84 65.728 67.948 210.377 1.00192.24 S ATOM 15191 SG CYSD8 87 65.087 70.576 208.117 1.00191.86 S Time building chain proxies: 6.46, per 1000 atoms: 0.23 Number of scatterers: 28391 At special positions: 0 Unit cell: (105.133, 152.72, 246.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 13 29.99 S 118 16.00 P 91 15.00 O 5684 8.00 N 4910 7.00 C 17575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 88 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 70 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 85 " pdb=" ZND11000 " pdb="ZN ZND11000 " - pdb=" SG CYSD1 84 " pdb="ZN ZND11000 " - pdb=" SG CYSD1 87 " pdb="ZN ZND11000 " - pdb=" SG CYSD1 71 " pdb="ZN ZND11000 " - pdb=" SG CYSD1 81 " pdb=" ZND21000 " pdb="ZN ZND21000 " - pdb=" SG CYSD2 87 " pdb="ZN ZND21000 " - pdb=" SG CYSD2 84 " pdb="ZN ZND21000 " - pdb=" SG CYSD2 71 " pdb="ZN ZND21000 " - pdb=" SG CYSD2 81 " pdb=" ZND31000 " pdb="ZN ZND31000 " - pdb=" SG CYSD3 84 " pdb="ZN ZND31000 " - pdb=" SG CYSD3 87 " pdb="ZN ZND31000 " - pdb=" SG CYSD3 71 " pdb="ZN ZND31000 " - pdb=" SG CYSD3 81 " pdb=" ZND41000 " pdb="ZN ZND41000 " - pdb=" SG CYSD4 71 " pdb="ZN ZND41000 " - pdb=" SG CYSD4 84 " pdb="ZN ZND41000 " - pdb=" SG CYSD4 81 " pdb="ZN ZND41000 " - pdb=" SG CYSD4 87 " pdb=" ZND51000 " pdb="ZN ZND51000 " - pdb=" SG CYSD5 84 " pdb="ZN ZND51000 " - pdb=" SG CYSD5 71 " pdb="ZN ZND51000 " - pdb=" SG CYSD5 81 " pdb="ZN ZND51000 " - pdb=" SG CYSD5 87 " pdb=" ZND61000 " pdb="ZN ZND61000 " - pdb=" SG CYSD6 87 " pdb="ZN ZND61000 " - pdb=" SG CYSD6 71 " pdb="ZN ZND61000 " - pdb=" SG CYSD6 84 " pdb="ZN ZND61000 " - pdb=" SG CYSD6 81 " pdb=" ZND71000 " pdb="ZN ZND71000 " - pdb=" SG CYSD7 84 " pdb="ZN ZND71000 " - pdb=" SG CYSD7 87 " pdb="ZN ZND71000 " - pdb=" SG CYSD7 71 " pdb="ZN ZND71000 " - pdb=" SG CYSD7 81 " pdb=" ZND81000 " pdb="ZN ZND81000 " - pdb=" SG CYSD8 84 " pdb="ZN ZND81000 " - pdb=" SG CYSD8 87 " pdb="ZN ZND81000 " - pdb=" SG CYSD8 71 " pdb="ZN ZND81000 " - pdb=" SG CYSD8 81 " pdb=" ZNE21000 " pdb="ZN ZNE21000 " - pdb=" NE2 HISE2 67 " pdb="ZN ZNE21000 " - pdb=" NE2 HISE2 397 " pdb=" ZNE21001 " pdb="ZN ZNE21001 " - pdb=" NE2 HISE2 62 " pdb="ZN ZNE21001 " - pdb=" ND1 HISE2 64 " pdb=" ZNE41000 " pdb="ZN ZNE41000 " - pdb=" NE2 HISE4 67 " pdb="ZN ZNE41000 " - pdb=" NE2 HISE4 397 " pdb=" ZNE41001 " pdb="ZN ZNE41001 " - pdb=" NE2 HISE4 62 " pdb="ZN ZNE41001 " - pdb=" ND1 HISE4 64 " pdb="ZN ZNE41001 " - pdb=" NE2 HISE4 148 " Number of angles added : 48 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6194 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 42 sheets defined 38.1% alpha, 23.7% beta 30 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'C' and resid 28 through 43 removed outlier: 3.522A pdb=" N LEU C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 removed outlier: 3.762A pdb=" N SER C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 52 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.848A pdb=" N SER C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'D1' and resid 24 through 32 Processing helix chain 'D1' and resid 51 through 66 Processing helix chain 'D1' and resid 74 through 78 Processing helix chain 'D1' and resid 84 through 91 Processing helix chain 'D1' and resid 109 through 113 Processing helix chain 'D1' and resid 156 through 172 Processing helix chain 'D1' and resid 176 through 180 Processing helix chain 'D1' and resid 194 through 199 Processing helix chain 'D2' and resid 24 through 32 Processing helix chain 'D2' and resid 51 through 66 Processing helix chain 'D2' and resid 84 through 91 Processing helix chain 'D2' and resid 109 through 113 Processing helix chain 'D2' and resid 156 through 172 Processing helix chain 'D2' and resid 176 through 180 Processing helix chain 'D2' and resid 196 through 199 Processing helix chain 'D3' and resid 24 through 32 Processing helix chain 'D3' and resid 51 through 66 Processing helix chain 'D3' and resid 84 through 91 Processing helix chain 'D3' and resid 109 through 113 Processing helix chain 'D3' and resid 156 through 172 Processing helix chain 'D3' and resid 176 through 180 Processing helix chain 'D3' and resid 196 through 199 Processing helix chain 'D4' and resid 24 through 32 Processing helix chain 'D4' and resid 51 through 66 Processing helix chain 'D4' and resid 84 through 91 Processing helix chain 'D4' and resid 109 through 113 Processing helix chain 'D4' and resid 156 through 172 Processing helix chain 'D4' and resid 176 through 180 Processing helix chain 'D4' and resid 196 through 199 Processing helix chain 'D5' and resid 24 through 32 Processing helix chain 'D5' and resid 51 through 66 Processing helix chain 'D5' and resid 84 through 91 Processing helix chain 'D5' and resid 109 through 113 Processing helix chain 'D5' and resid 156 through 172 Processing helix chain 'D5' and resid 176 through 180 Processing helix chain 'D5' and resid 194 through 199 removed outlier: 4.582A pdb=" N PHED5 198 " --> pdb=" O THRD5 195 " (cutoff:3.500A) Processing helix chain 'D6' and resid 24 through 32 Processing helix chain 'D6' and resid 51 through 66 Processing helix chain 'D6' and resid 84 through 90 Processing helix chain 'D6' and resid 109 through 113 Processing helix chain 'D6' and resid 156 through 172 Processing helix chain 'D6' and resid 176 through 180 Processing helix chain 'D6' and resid 194 through 199 removed outlier: 4.373A pdb=" N PHED6 198 " --> pdb=" O THRD6 195 " (cutoff:3.500A) Processing helix chain 'D7' and resid 24 through 32 Processing helix chain 'D7' and resid 51 through 66 Processing helix chain 'D7' and resid 84 through 91 Processing helix chain 'D7' and resid 109 through 113 Processing helix chain 'D7' and resid 156 through 172 Processing helix chain 'D7' and resid 176 through 180 Processing helix chain 'D8' and resid 51 through 66 Processing helix chain 'D8' and resid 74 through 78 Processing helix chain 'D8' and resid 84 through 91 Processing helix chain 'D8' and resid 109 through 113 Processing helix chain 'D8' and resid 156 through 172 Processing helix chain 'D8' and resid 176 through 180 Processing helix chain 'E1' and resid 470 through 488 removed outlier: 3.523A pdb=" N PHEE1 474 " --> pdb=" O ASPE1 470 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLNE1 488 " --> pdb=" O LYSE1 484 " (cutoff:3.500A) Processing helix chain 'E1' and resid 509 through 523 Processing helix chain 'E1' and resid 527 through 541 Processing helix chain 'E1' and resid 541 through 554 Processing helix chain 'E1' and resid 572 through 591 Processing helix chain 'E1' and resid 594 through 603 Processing helix chain 'E2' and resid 37 through 53 removed outlier: 3.736A pdb=" N ASNE2 41 " --> pdb=" O ILEE2 37 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASNE2 42 " --> pdb=" O GLUE2 38 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLUE2 43 " --> pdb=" O LYSE2 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEE2 52 " --> pdb=" O LYSE2 48 " (cutoff:3.500A) Processing helix chain 'E2' and resid 64 through 69 Processing helix chain 'E2' and resid 70 through 77 Processing helix chain 'E2' and resid 86 through 107 Processing helix chain 'E2' and resid 114 through 123 removed outlier: 3.593A pdb=" N PHEE2 122 " --> pdb=" O ILEE2 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUE2 123 " --> pdb=" O GLUE2 119 " (cutoff:3.500A) Processing helix chain 'E2' and resid 206 through 222 removed outlier: 3.610A pdb=" N ARGE2 210 " --> pdb=" O SERE2 206 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEUE2 212 " --> pdb=" O ARGE2 208 " (cutoff:3.500A) Processing helix chain 'E2' and resid 233 through 245 removed outlier: 3.526A pdb=" N TYRE2 245 " --> pdb=" O THRE2 241 " (cutoff:3.500A) Processing helix chain 'E2' and resid 255 through 269 removed outlier: 3.972A pdb=" N LYSE2 266 " --> pdb=" O THRE2 262 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLUE2 267 " --> pdb=" O ASNE2 263 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYRE2 268 " --> pdb=" O LEUE2 264 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASNE2 269 " --> pdb=" O ILEE2 265 " (cutoff:3.500A) Processing helix chain 'E2' and resid 273 through 278 removed outlier: 3.760A pdb=" N ARGE2 278 " --> pdb=" O LYSE2 274 " (cutoff:3.500A) Processing helix chain 'E2' and resid 295 through 304 Processing helix chain 'E2' and resid 323 through 331 removed outlier: 4.226A pdb=" N GLUE2 328 " --> pdb=" O LEUE2 324 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLNE2 329 " --> pdb=" O ASNE2 325 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILEE2 330 " --> pdb=" O HISE2 326 " (cutoff:3.500A) Processing helix chain 'E2' and resid 348 through 355 Processing helix chain 'E2' and resid 375 through 386 removed outlier: 3.682A pdb=" N LEUE2 386 " --> pdb=" O TYRE2 382 " (cutoff:3.500A) Processing helix chain 'E2' and resid 399 through 413 removed outlier: 3.577A pdb=" N LYSE2 408 " --> pdb=" O GLUE2 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARGE2 409 " --> pdb=" O ILEE2 405 " (cutoff:3.500A) Processing helix chain 'E2' and resid 470 through 489 removed outlier: 3.564A pdb=" N PHEE2 474 " --> pdb=" O ASPE2 470 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILEE2 489 " --> pdb=" O METE2 485 " (cutoff:3.500A) Processing helix chain 'E2' and resid 509 through 523 Processing helix chain 'E2' and resid 527 through 541 Processing helix chain 'E2' and resid 541 through 554 Processing helix chain 'E2' and resid 572 through 591 Processing helix chain 'E2' and resid 594 through 603 Processing helix chain 'E3' and resid 470 through 490 removed outlier: 3.519A pdb=" N PHEE3 474 " --> pdb=" O ASPE3 470 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILEE3 489 " --> pdb=" O METE3 485 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VALE3 490 " --> pdb=" O ARGE3 486 " (cutoff:3.500A) Processing helix chain 'E3' and resid 509 through 523 Processing helix chain 'E3' and resid 527 through 541 Processing helix chain 'E3' and resid 541 through 554 Processing helix chain 'E3' and resid 572 through 591 Processing helix chain 'E3' and resid 594 through 603 Processing helix chain 'E4' and resid 39 through 53 removed outlier: 4.100A pdb=" N GLUE4 43 " --> pdb=" O LYSE4 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILEE4 52 " --> pdb=" O LYSE4 48 " (cutoff:3.500A) Processing helix chain 'E4' and resid 64 through 69 Processing helix chain 'E4' and resid 70 through 77 Processing helix chain 'E4' and resid 86 through 107 Processing helix chain 'E4' and resid 114 through 123 removed outlier: 3.593A pdb=" N PHEE4 122 " --> pdb=" O ILEE4 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLUE4 123 " --> pdb=" O GLUE4 119 " (cutoff:3.500A) Processing helix chain 'E4' and resid 206 through 222 removed outlier: 3.697A pdb=" N ARGE4 210 " --> pdb=" O SERE4 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEUE4 212 " --> pdb=" O ARGE4 208 " (cutoff:3.500A) Processing helix chain 'E4' and resid 233 through 245 removed outlier: 3.512A pdb=" N TYRE4 245 " --> pdb=" O THRE4 241 " (cutoff:3.500A) Processing helix chain 'E4' and resid 255 through 268 Processing helix chain 'E4' and resid 269 through 272 Processing helix chain 'E4' and resid 273 through 278 removed outlier: 3.750A pdb=" N ARGE4 278 " --> pdb=" O LYSE4 274 " (cutoff:3.500A) Processing helix chain 'E4' and resid 295 through 304 Processing helix chain 'E4' and resid 323 through 331 removed outlier: 4.233A pdb=" N GLUE4 328 " --> pdb=" O LEUE4 324 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLNE4 329 " --> pdb=" O ASNE4 325 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILEE4 330 " --> pdb=" O HISE4 326 " (cutoff:3.500A) Processing helix chain 'E4' and resid 348 through 355 Processing helix chain 'E4' and resid 375 through 386 removed outlier: 3.678A pdb=" N LEUE4 386 " --> pdb=" O TYRE4 382 " (cutoff:3.500A) Processing helix chain 'E4' and resid 399 through 413 removed outlier: 3.576A pdb=" N LYSE4 408 " --> pdb=" O GLUE4 404 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGE4 409 " --> pdb=" O ILEE4 405 " (cutoff:3.500A) Processing helix chain 'E4' and resid 471 through 480 Processing helix chain 'E4' and resid 509 through 523 Processing helix chain 'E4' and resid 527 through 541 Processing helix chain 'E4' and resid 541 through 554 Processing helix chain 'E4' and resid 572 through 591 Processing helix chain 'E4' and resid 594 through 603 Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.555A pdb=" N ILE C 120 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 160 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU C 9 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 158 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 102 removed outlier: 3.565A pdb=" N TYR C 107 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 214 through 216 Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 195 Processing sheet with id=AA6, first strand: chain 'D1' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'D1' and resid 48 through 49 removed outlier: 3.791A pdb=" N METD1 5 " --> pdb=" O VALD1 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D1' and resid 114 through 122 removed outlier: 3.501A pdb=" N ASPD1 131 " --> pdb=" O ARGD1 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D2' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'D2' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'D2' and resid 114 through 122 Processing sheet with id=AB3, first strand: chain 'D3' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'D3' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'D3' and resid 114 through 122 Processing sheet with id=AB6, first strand: chain 'D4' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'D4' and resid 48 through 49 Processing sheet with id=AB8, first strand: chain 'D4' and resid 114 through 122 removed outlier: 3.514A pdb=" N ASPD4 131 " --> pdb=" O ARGD4 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D5' and resid 48 through 49 Processing sheet with id=AC1, first strand: chain 'D5' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'D5' and resid 114 through 122 Processing sheet with id=AC3, first strand: chain 'D6' and resid 48 through 49 Processing sheet with id=AC4, first strand: chain 'D6' and resid 48 through 49 Processing sheet with id=AC5, first strand: chain 'D6' and resid 91 through 92 Processing sheet with id=AC6, first strand: chain 'D6' and resid 114 through 122 removed outlier: 3.528A pdb=" N ASPD6 131 " --> pdb=" O ARGD6 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D7' and resid 48 through 49 Processing sheet with id=AC8, first strand: chain 'D7' and resid 48 through 49 removed outlier: 3.651A pdb=" N METD7 5 " --> pdb=" O VALD7 193 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D7' and resid 114 through 122 removed outlier: 3.503A pdb=" N ASPD7 131 " --> pdb=" O ARGD7 121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D8' and resid 48 through 49 Processing sheet with id=AD2, first strand: chain 'D8' and resid 48 through 49 removed outlier: 3.694A pdb=" N METD8 5 " --> pdb=" O VALD8 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D8' and resid 114 through 115 Processing sheet with id=AD4, first strand: chain 'E1' and resid 435 through 437 removed outlier: 3.523A pdb=" N ILEE1 468 " --> pdb=" O VALE1 436 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGE3 451 " --> pdb=" O GLUE1 461 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILEE3 468 " --> pdb=" O VALE3 436 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASNE3 438 " --> pdb=" O ILEE3 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E1' and resid 435 through 437 removed outlier: 3.523A pdb=" N ILEE1 468 " --> pdb=" O VALE1 436 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGE3 451 " --> pdb=" O GLUE1 461 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E1' and resid 445 through 447 Processing sheet with id=AD7, first strand: chain 'E2' and resid 2 through 6 removed outlier: 6.219A pdb=" N ALAE2 15 " --> pdb=" O ILEE2 5 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYSE2 24 " --> pdb=" O ILEE2 57 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILEE2 59 " --> pdb=" O LYSE2 24 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEUE2 26 " --> pdb=" O ILEE2 59 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASPE2 56 " --> pdb=" O LYSE2 82 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILEE2 84 " --> pdb=" O ASPE2 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYSE2 58 " --> pdb=" O ILEE2 84 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASPE2 126 " --> pdb=" O ASNE2 81 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILEE2 83 " --> pdb=" O ASPE2 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E2' and resid 134 through 135 Processing sheet with id=AD9, first strand: chain 'E2' and resid 143 through 145 removed outlier: 6.335A pdb=" N ASNE2 163 " --> pdb=" O TYRE2 191 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILEE2 193 " --> pdb=" O ASNE2 163 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEUE2 165 " --> pdb=" O ILEE2 193 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLUE2 195 " --> pdb=" O LEUE2 165 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E2' and resid 291 through 292 removed outlier: 6.527A pdb=" N VALE2 225 " --> pdb=" O ILEE2 311 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SERE2 313 " --> pdb=" O VALE2 225 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILEE2 227 " --> pdb=" O SERE2 313 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYSE2 224 " --> pdb=" O THRE2 337 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILEE2 339 " --> pdb=" O LYSE2 224 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEUE2 226 " --> pdb=" O ILEE2 339 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E2' and resid 434 through 437 removed outlier: 4.134A pdb=" N ARGE2 451 " --> pdb=" O GLUE4 461 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARGE4 451 " --> pdb=" O GLUE2 461 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGE4 465 " --> pdb=" O LYSE4 462 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E2' and resid 445 through 447 removed outlier: 4.134A pdb=" N ARGE2 451 " --> pdb=" O GLUE4 461 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARGE4 451 " --> pdb=" O GLUE2 461 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E4' and resid 125 through 127 removed outlier: 7.902A pdb=" N ASPE4 126 " --> pdb=" O ASNE4 81 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILEE4 83 " --> pdb=" O ASPE4 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASPE4 56 " --> pdb=" O LYSE4 82 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILEE4 84 " --> pdb=" O ASPE4 56 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYSE4 58 " --> pdb=" O ILEE4 84 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYSE4 24 " --> pdb=" O ILEE4 57 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILEE4 59 " --> pdb=" O LYSE4 24 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEUE4 26 " --> pdb=" O ILEE4 59 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALAE4 15 " --> pdb=" O ILEE4 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E4' and resid 134 through 135 removed outlier: 6.381A pdb=" N ASNE4 163 " --> pdb=" O TYRE4 191 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILEE4 193 " --> pdb=" O ASNE4 163 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEUE4 165 " --> pdb=" O ILEE4 193 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLUE4 195 " --> pdb=" O LEUE4 165 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E4' and resid 291 through 292 removed outlier: 6.546A pdb=" N VALE4 225 " --> pdb=" O ILEE4 311 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SERE4 313 " --> pdb=" O VALE4 225 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILEE4 227 " --> pdb=" O SERE4 313 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYSE4 224 " --> pdb=" O THRE4 337 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILEE4 339 " --> pdb=" O LYSE4 224 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEUE4 226 " --> pdb=" O ILEE4 339 " (cutoff:3.500A) 1248 hydrogen bonds defined for protein. 3510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 6.33 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5484 1.34 - 1.46: 7286 1.46 - 1.58: 15687 1.58 - 1.69: 386 1.69 - 1.81: 183 Bond restraints: 29026 Sorted by residual: bond pdb=" CB ILEE1 523 " pdb=" CG1 ILEE1 523 " ideal model delta sigma weight residual 1.530 1.595 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C PHEE2 249 " pdb=" N PROE2 250 " ideal model delta sigma weight residual 1.333 1.371 -0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" C LEU C 167 " pdb=" N PRO C 168 " ideal model delta sigma weight residual 1.330 1.369 -0.039 1.22e-02 6.72e+03 1.03e+01 bond pdb=" C LEUE2 505 " pdb=" N PROE2 506 " ideal model delta sigma weight residual 1.329 1.370 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" C ILEE2 110 " pdb=" N PROE2 111 " ideal model delta sigma weight residual 1.330 1.369 -0.039 1.22e-02 6.72e+03 1.02e+01 ... (remaining 29021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 32354 2.42 - 4.83: 6130 4.83 - 7.25: 933 7.25 - 9.67: 46 9.67 - 12.09: 1 Bond angle restraints: 39464 Sorted by residual: angle pdb=" CA PHED7 51 " pdb=" CB PHED7 51 " pdb=" CG PHED7 51 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.01e+01 angle pdb=" CA PHED8 51 " pdb=" CB PHED8 51 " pdb=" CG PHED8 51 " ideal model delta sigma weight residual 113.80 120.84 -7.04 1.00e+00 1.00e+00 4.95e+01 angle pdb=" C ASPD3 102 " pdb=" CA ASPD3 102 " pdb=" CB ASPD3 102 " ideal model delta sigma weight residual 109.83 121.92 -12.09 1.75e+00 3.27e-01 4.77e+01 angle pdb=" C ASND7 152 " pdb=" CA ASND7 152 " pdb=" CB ASND7 152 " ideal model delta sigma weight residual 111.00 116.81 -5.81 8.70e-01 1.32e+00 4.45e+01 angle pdb=" CA PHED1 51 " pdb=" CB PHED1 51 " pdb=" CG PHED1 51 " ideal model delta sigma weight residual 113.80 120.45 -6.65 1.00e+00 1.00e+00 4.42e+01 ... (remaining 39459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 16137 17.24 - 34.48: 1284 34.48 - 51.73: 215 51.73 - 68.97: 159 68.97 - 86.21: 89 Dihedral angle restraints: 17884 sinusoidal: 8299 harmonic: 9585 Sorted by residual: dihedral pdb=" C5' U A 50 " pdb=" C4' U A 50 " pdb=" C3' U A 50 " pdb=" O3' U A 50 " ideal model delta sinusoidal sigma weight residual 147.00 98.30 48.70 1 8.00e+00 1.56e-02 5.10e+01 dihedral pdb=" C5' C B 49 " pdb=" C4' C B 49 " pdb=" C3' C B 49 " pdb=" O3' C B 49 " ideal model delta sinusoidal sigma weight residual 147.00 100.73 46.27 1 8.00e+00 1.56e-02 4.63e+01 dihedral pdb=" C ASPD3 102 " pdb=" N ASPD3 102 " pdb=" CA ASPD3 102 " pdb=" CB ASPD3 102 " ideal model delta harmonic sigma weight residual -122.60 -139.11 16.51 0 2.50e+00 1.60e-01 4.36e+01 ... (remaining 17881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3639 0.117 - 0.235: 810 0.235 - 0.352: 22 0.352 - 0.469: 2 0.469 - 0.586: 3 Chirality restraints: 4476 Sorted by residual: chirality pdb=" CA ASPD4 102 " pdb=" N ASPD4 102 " pdb=" C ASPD4 102 " pdb=" CB ASPD4 102 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" CA ASPD3 102 " pdb=" N ASPD3 102 " pdb=" C ASPD3 102 " pdb=" CB ASPD3 102 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" P C B 28 " pdb=" OP1 C B 28 " pdb=" OP2 C B 28 " pdb=" O5' C B 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 4473 not shown) Planarity restraints: 4733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 26 " -0.046 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G A 26 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G A 26 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G A 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 26 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G A 26 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G A 26 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A 26 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G A 26 " -0.026 2.00e-02 2.50e+03 pdb=" N2 G A 26 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G A 26 " 0.030 2.00e-02 2.50e+03 pdb=" C4 G A 26 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 48 " -0.039 2.00e-02 2.50e+03 1.89e-02 1.07e+01 pdb=" N9 G B 48 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 48 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 48 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G B 48 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G B 48 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 48 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 48 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G B 48 " -0.029 2.00e-02 2.50e+03 pdb=" N2 G B 48 " 0.019 2.00e-02 2.50e+03 pdb=" N3 G B 48 " 0.026 2.00e-02 2.50e+03 pdb=" C4 G B 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 54 " -0.040 2.00e-02 2.50e+03 1.86e-02 1.04e+01 pdb=" N9 G B 54 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G B 54 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 54 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 54 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 54 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 54 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 54 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G B 54 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 54 " 0.038 2.00e-02 2.50e+03 pdb=" C4 G B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 4730 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 90 2.61 - 3.19: 20795 3.19 - 3.76: 42644 3.76 - 4.33: 62201 4.33 - 4.90: 99768 Nonbonded interactions: 225498 Sorted by model distance: nonbonded pdb=" OD2 ASPE2 66 " pdb="ZN ZNE21000 " model vdw 2.043 2.230 nonbonded pdb=" OD2 ASPE2 169 " pdb="ZN ZNE21001 " model vdw 2.056 2.230 nonbonded pdb=" OD2 ASPE4 66 " pdb="ZN ZNE41000 " model vdw 2.162 2.230 nonbonded pdb=" OD2 ASPE4 169 " pdb="ZN ZNE41000 " model vdw 2.165 2.230 nonbonded pdb=" O2' A A 20 " pdb=" O LEUD2 120 " model vdw 2.472 3.040 ... (remaining 225493 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 'D1' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D2' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D3' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D4' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D5' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D6' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = (chain 'D7' and (resid 4 through 27 or resid 36 through 116 or resid 135 through \ 1000)) selection = chain 'D8' } ncs_group { reference = chain 'E1' selection = chain 'E3' } ncs_group { reference = (chain 'E2' and (resid 1 through 35 or resid 38 through 480 or resid 505 through \ 1001)) selection = (chain 'E4' and (resid 1 through 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 1001)) } 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.320 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.013 0.355 29070 Z= 0.731 Angle : 1.944 12.086 39512 Z= 1.237 Chirality : 0.088 0.586 4476 Planarity : 0.005 0.031 4733 Dihedral : 15.279 86.209 11690 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 1.02 % Allowed : 3.48 % Favored : 95.49 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % Twisted Proline : 1.05 % 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 (0.13), residues: 3266 helix: 0.16 (0.14), residues: 1063 sheet: 1.16 (0.20), residues: 655 loop : -1.44 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARGD3 56 TYR 0.021 0.003 TYRE1 450 PHE 0.025 0.003 PHED6 133 TRP 0.014 0.003 TRPE4 535 HIS 0.013 0.002 HISE4 397 Details of bonding type rmsd covalent geometry : bond 0.01181 (29026) covalent geometry : angle 1.92903 (39464) hydrogen bonds : bond 0.19698 ( 1264) hydrogen bonds : angle 6.67676 ( 3650) metal coordination : bond 0.11880 ( 44) metal coordination : angle 7.18573 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 564 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6683 (ttp) cc_final: 0.4670 (ttm) REVERT: C 136 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8305 (ttp80) REVERT: D1 157 ASP cc_start: 0.7557 (m-30) cc_final: 0.7355 (m-30) REVERT: D5 56 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8880 (ttt180) REVERT: D6 132 THR cc_start: 0.7587 (m) cc_final: 0.7301 (p) REVERT: D7 40 ARG cc_start: 0.6871 (ttm-80) cc_final: 0.6665 (ttm-80) REVERT: D8 60 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6362 (mt-10) REVERT: D8 101 VAL cc_start: 0.7233 (t) cc_final: 0.6959 (t) REVERT: D8 166 LYS cc_start: 0.8530 (mttt) cc_final: 0.7990 (pptt) REVERT: D8 188 VAL cc_start: 0.6530 (t) cc_final: 0.6009 (t) REVERT: E2 47 LYS cc_start: 0.8775 (tttt) cc_final: 0.8483 (tmtt) REVERT: E2 71 VAL cc_start: 0.9324 (t) cc_final: 0.9104 (t) REVERT: E2 100 PHE cc_start: 0.8483 (t80) cc_final: 0.8244 (t80) REVERT: E2 184 MET cc_start: 0.7908 (ptp) cc_final: 0.7526 (mtm) REVERT: E2 230 PHE cc_start: 0.8176 (t80) cc_final: 0.7780 (t80) REVERT: E2 297 ASN cc_start: 0.7737 (m-40) cc_final: 0.7527 (p0) REVERT: E3 451 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7815 (mmm160) REVERT: E3 470 ASP cc_start: 0.7953 (p0) cc_final: 0.7657 (p0) REVERT: E4 453 MET cc_start: 0.8520 (ttt) cc_final: 0.7818 (ttm) outliers start: 30 outliers final: 1 residues processed: 588 average time/residue: 0.8989 time to fit residues: 597.8365 Evaluate side-chains 307 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D4 residue 26 GLU Chi-restraints excluded: chain D5 residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 ASN D3 154 GLN E2 104 GLN E2 148 HIS E2 175 GLN E2 498 GLN E2 553 HIS E2 574 ASN E3 443 ASN E4 529 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.071726 restraints weight = 54644.057| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.94 r_work: 0.2800 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29070 Z= 0.147 Angle : 0.641 11.540 39512 Z= 0.335 Chirality : 0.044 0.245 4476 Planarity : 0.004 0.051 4733 Dihedral : 12.574 77.667 4965 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.25 % Rotamer: Outliers : 2.05 % Allowed : 12.36 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 0.77 (0.14), residues: 3266 helix: 2.05 (0.16), residues: 1074 sheet: 1.06 (0.19), residues: 687 loop : -0.92 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGE1 465 TYR 0.023 0.001 TYRE2 115 PHE 0.020 0.002 PHED7 51 TRP 0.022 0.001 TRPE4 478 HIS 0.005 0.001 HISE2 62 Details of bonding type rmsd covalent geometry : bond 0.00318 (29026) covalent geometry : angle 0.62245 (39464) hydrogen bonds : bond 0.04583 ( 1264) hydrogen bonds : angle 4.68031 ( 3650) metal coordination : bond 0.00716 ( 44) metal coordination : angle 4.39892 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.8623 (tt0) cc_final: 0.8277 (pt0) REVERT: C 125 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: C 136 ARG cc_start: 0.9191 (ttp-170) cc_final: 0.8898 (ttp80) REVERT: D1 5 MET cc_start: 0.7710 (mtm) cc_final: 0.7498 (ptp) REVERT: D1 12 MET cc_start: 0.9174 (ttp) cc_final: 0.8913 (ttp) REVERT: D1 157 ASP cc_start: 0.8314 (m-30) cc_final: 0.7888 (m-30) REVERT: D2 95 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8140 (ttm-80) REVERT: D3 62 MET cc_start: 0.9157 (mtm) cc_final: 0.8875 (mtm) REVERT: D3 69 ASN cc_start: 0.8852 (p0) cc_final: 0.8397 (p0) REVERT: D4 125 GLN cc_start: 0.8601 (tp40) cc_final: 0.8309 (tp40) REVERT: D5 5 MET cc_start: 0.8365 (mtm) cc_final: 0.8030 (mtp) REVERT: D6 154 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: D8 24 ARG cc_start: 0.3113 (mtt180) cc_final: 0.2400 (mtt90) REVERT: D8 60 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6379 (tt0) REVERT: D8 93 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5699 (mmm) REVERT: D8 166 LYS cc_start: 0.8360 (mttt) cc_final: 0.7998 (pttp) REVERT: E1 436 VAL cc_start: 0.8625 (t) cc_final: 0.8306 (m) REVERT: E1 508 MET cc_start: 0.6237 (ptm) cc_final: 0.5847 (ptm) REVERT: E2 33 GLN cc_start: 0.8193 (mm110) cc_final: 0.7592 (tp40) REVERT: E2 47 LYS cc_start: 0.9271 (tttt) cc_final: 0.8729 (tmtt) REVERT: E2 150 ILE cc_start: 0.8515 (mm) cc_final: 0.8252 (mp) REVERT: E2 184 MET cc_start: 0.8447 (ptp) cc_final: 0.7802 (mtm) REVERT: E2 230 PHE cc_start: 0.8638 (t80) cc_final: 0.7750 (t80) REVERT: E2 272 LEU cc_start: 0.8134 (mm) cc_final: 0.7894 (mm) REVERT: E2 286 PHE cc_start: 0.7279 (m-80) cc_final: 0.7076 (m-80) REVERT: E2 290 TYR cc_start: 0.5917 (p90) cc_final: 0.5628 (p90) REVERT: E2 297 ASN cc_start: 0.8042 (m-40) cc_final: 0.7768 (p0) REVERT: E2 444 MET cc_start: 0.8716 (tpp) cc_final: 0.8469 (tpp) REVERT: E3 470 ASP cc_start: 0.8306 (p0) cc_final: 0.8032 (p0) REVERT: E3 486 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6879 (mtm110) REVERT: E3 527 SER cc_start: 0.8824 (m) cc_final: 0.8465 (p) REVERT: E4 28 ASP cc_start: 0.8628 (m-30) cc_final: 0.8409 (m-30) REVERT: E4 434 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8181 (mmmt) REVERT: E4 453 MET cc_start: 0.9076 (ttt) cc_final: 0.8840 (ttm) REVERT: E4 461 GLU cc_start: 0.7694 (pp20) cc_final: 0.7395 (pp20) outliers start: 60 outliers final: 13 residues processed: 362 average time/residue: 0.8384 time to fit residues: 344.9899 Evaluate side-chains 295 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D6 residue 111 GLU Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D8 residue 39 VAL Chi-restraints excluded: chain D8 residue 93 MET Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain D8 residue 185 SER Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E3 residue 485 MET Chi-restraints excluded: chain E4 residue 434 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 150 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 327 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 281 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 ASN D1 162 GLN D2 45 ASN D4 45 ASN ** E2 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070716 restraints weight = 54838.332| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.85 r_work: 0.2776 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29070 Z= 0.144 Angle : 0.574 9.741 39512 Z= 0.296 Chirality : 0.042 0.218 4476 Planarity : 0.003 0.050 4733 Dihedral : 12.324 77.774 4958 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.05 % Allowed : 13.69 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.06 (0.14), residues: 3266 helix: 2.34 (0.15), residues: 1074 sheet: 1.26 (0.19), residues: 678 loop : -0.82 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARGD8 56 TYR 0.018 0.001 TYRE2 115 PHE 0.029 0.002 PHED7 167 TRP 0.010 0.001 TRPD6 176 HIS 0.003 0.001 HISE4 510 Details of bonding type rmsd covalent geometry : bond 0.00324 (29026) covalent geometry : angle 0.55499 (39464) hydrogen bonds : bond 0.03946 ( 1264) hydrogen bonds : angle 4.39184 ( 3650) metal coordination : bond 0.00621 ( 44) metal coordination : angle 4.25266 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ARG cc_start: 0.9200 (ttp-170) cc_final: 0.8847 (ttp80) REVERT: D1 12 MET cc_start: 0.9145 (ttp) cc_final: 0.8848 (ttp) REVERT: D1 102 ASP cc_start: 0.8916 (t0) cc_final: 0.8630 (t0) REVERT: D1 156 LYS cc_start: 0.8189 (mppt) cc_final: 0.7877 (ttmm) REVERT: D1 157 ASP cc_start: 0.8602 (m-30) cc_final: 0.8318 (m-30) REVERT: D2 5 MET cc_start: 0.8954 (mtm) cc_final: 0.8503 (mtm) REVERT: D2 95 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8185 (ttm-80) REVERT: D3 62 MET cc_start: 0.9211 (mtm) cc_final: 0.8900 (mtm) REVERT: D3 69 ASN cc_start: 0.8940 (p0) cc_final: 0.8435 (p0) REVERT: D4 125 GLN cc_start: 0.8608 (tp40) cc_final: 0.8382 (tp40) REVERT: D5 5 MET cc_start: 0.8479 (mtm) cc_final: 0.8188 (mtm) REVERT: D6 132 THR cc_start: 0.7501 (m) cc_final: 0.7288 (p) REVERT: D6 154 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: D8 75 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6786 (pm20) REVERT: D8 79 ARG cc_start: 0.5984 (tpp-160) cc_final: 0.5746 (tpp-160) REVERT: D8 83 ARG cc_start: 0.6628 (tpm170) cc_final: 0.6420 (tpm170) REVERT: D8 89 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6323 (tm) REVERT: D8 93 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.4887 (mmm) REVERT: D8 166 LYS cc_start: 0.8451 (mttt) cc_final: 0.8070 (pttp) REVERT: E1 436 VAL cc_start: 0.8694 (t) cc_final: 0.8331 (m) REVERT: E1 508 MET cc_start: 0.5960 (ptm) cc_final: 0.5633 (ptm) REVERT: E2 28 ASP cc_start: 0.8105 (m-30) cc_final: 0.7723 (t0) REVERT: E2 33 GLN cc_start: 0.8018 (mm110) cc_final: 0.7491 (tp40) REVERT: E2 47 LYS cc_start: 0.9203 (tttt) cc_final: 0.8689 (tmtt) REVERT: E2 150 ILE cc_start: 0.8403 (mm) cc_final: 0.8083 (mp) REVERT: E2 184 MET cc_start: 0.8351 (ptp) cc_final: 0.7754 (mtm) REVERT: E2 230 PHE cc_start: 0.8517 (t80) cc_final: 0.7581 (t80) REVERT: E2 269 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8100 (p0) REVERT: E2 272 LEU cc_start: 0.8174 (mm) cc_final: 0.7931 (mm) REVERT: E2 286 PHE cc_start: 0.7319 (m-80) cc_final: 0.7079 (m-80) REVERT: E2 297 ASN cc_start: 0.8041 (m-40) cc_final: 0.7771 (p0) REVERT: E2 367 LEU cc_start: 0.7783 (tt) cc_final: 0.6715 (tt) REVERT: E2 402 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: E2 503 MET cc_start: 0.7177 (mpt) cc_final: 0.6922 (mpp) REVERT: E3 470 ASP cc_start: 0.8488 (p0) cc_final: 0.8160 (p0) REVERT: E3 522 ASN cc_start: 0.9042 (m-40) cc_final: 0.8715 (m-40) REVERT: E3 527 SER cc_start: 0.8907 (m) cc_final: 0.8586 (p) REVERT: E4 354 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8338 (pp) REVERT: E4 453 MET cc_start: 0.9115 (ttt) cc_final: 0.8909 (ttm) outliers start: 60 outliers final: 17 residues processed: 329 average time/residue: 0.7429 time to fit residues: 283.2121 Evaluate side-chains 291 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D3 residue 123 GLU Chi-restraints excluded: chain D4 residue 39 VAL Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 70 VAL Chi-restraints excluded: chain D8 residue 89 LEU Chi-restraints excluded: chain D8 residue 93 MET Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 269 ASN Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E2 residue 453 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 354 LEU Chi-restraints excluded: chain E4 residue 471 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 251 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 237 optimal weight: 0.3980 chunk 219 optimal weight: 40.0000 chunk 91 optimal weight: 0.0570 chunk 37 optimal weight: 5.9990 overall best weight: 2.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1 162 GLN D2 45 ASN D4 45 ASN E1 553 HIS E2 175 GLN E2 373 HIS E3 553 HIS E4 161 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.067865 restraints weight = 54854.861| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.88 r_work: 0.2716 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29070 Z= 0.223 Angle : 0.602 9.958 39512 Z= 0.309 Chirality : 0.043 0.244 4476 Planarity : 0.004 0.070 4733 Dihedral : 12.212 77.727 4958 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 13.83 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.06 (0.14), residues: 3266 helix: 2.40 (0.15), residues: 1074 sheet: 1.21 (0.19), residues: 696 loop : -0.86 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGE1 465 TYR 0.015 0.001 TYRE2 388 PHE 0.019 0.002 PHED6 133 TRP 0.016 0.001 TRPE4 478 HIS 0.005 0.001 HISE4 62 Details of bonding type rmsd covalent geometry : bond 0.00514 (29026) covalent geometry : angle 0.58564 (39464) hydrogen bonds : bond 0.04148 ( 1264) hydrogen bonds : angle 4.38280 ( 3650) metal coordination : bond 0.00900 ( 44) metal coordination : angle 4.08512 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ARG cc_start: 0.9271 (ttp-170) cc_final: 0.8885 (ttp80) REVERT: D1 12 MET cc_start: 0.9114 (ttp) cc_final: 0.8808 (ttp) REVERT: D1 102 ASP cc_start: 0.8915 (t0) cc_final: 0.8627 (t0) REVERT: D1 157 ASP cc_start: 0.8579 (m-30) cc_final: 0.8375 (m-30) REVERT: D2 5 MET cc_start: 0.8882 (mtm) cc_final: 0.8438 (mtm) REVERT: D3 62 MET cc_start: 0.9238 (mtm) cc_final: 0.8848 (mtm) REVERT: D3 69 ASN cc_start: 0.9008 (p0) cc_final: 0.8575 (p0) REVERT: D5 5 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8156 (mtp) REVERT: D6 154 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: D7 29 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: D7 72 ASP cc_start: 0.8057 (p0) cc_final: 0.7723 (t70) REVERT: D8 6 LYS cc_start: 0.4490 (mppt) cc_final: 0.3833 (mttp) REVERT: D8 40 ARG cc_start: 0.5612 (ttm170) cc_final: 0.5370 (ptt180) REVERT: D8 79 ARG cc_start: 0.6180 (tpp-160) cc_final: 0.5370 (mmp-170) REVERT: D8 83 ARG cc_start: 0.6581 (tpm170) cc_final: 0.6318 (tpm170) REVERT: D8 136 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6259 (mp0) REVERT: D8 166 LYS cc_start: 0.8471 (mttt) cc_final: 0.8073 (pttp) REVERT: E1 436 VAL cc_start: 0.8668 (t) cc_final: 0.8387 (p) REVERT: E1 465 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6057 (pmm-80) REVERT: E1 485 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8898 (tmm) REVERT: E1 508 MET cc_start: 0.6174 (ptm) cc_final: 0.5804 (ptm) REVERT: E1 609 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (tp) REVERT: E2 28 ASP cc_start: 0.8167 (m-30) cc_final: 0.7730 (t0) REVERT: E2 33 GLN cc_start: 0.7841 (mm110) cc_final: 0.7460 (tp40) REVERT: E2 47 LYS cc_start: 0.9272 (tttt) cc_final: 0.8770 (ptmm) REVERT: E2 184 MET cc_start: 0.8426 (ptp) cc_final: 0.7693 (mtm) REVERT: E2 230 PHE cc_start: 0.8444 (t80) cc_final: 0.7422 (t80) REVERT: E2 272 LEU cc_start: 0.8267 (mm) cc_final: 0.7921 (mm) REVERT: E2 286 PHE cc_start: 0.7479 (m-80) cc_final: 0.7226 (m-80) REVERT: E2 290 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.6116 (p90) REVERT: E2 297 ASN cc_start: 0.7956 (m-40) cc_final: 0.7658 (p0) REVERT: E2 367 LEU cc_start: 0.8067 (tt) cc_final: 0.5981 (tt) REVERT: E2 444 MET cc_start: 0.9249 (tpp) cc_final: 0.8015 (tpp) REVERT: E2 480 GLU cc_start: 0.8447 (tp30) cc_final: 0.8240 (tp30) REVERT: E2 483 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8632 (m-40) REVERT: E2 503 MET cc_start: 0.7066 (mpt) cc_final: 0.6801 (mpp) REVERT: E3 470 ASP cc_start: 0.8648 (p0) cc_final: 0.8261 (p0) REVERT: E3 485 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8098 (mmp) REVERT: E3 522 ASN cc_start: 0.9024 (m-40) cc_final: 0.8713 (m-40) REVERT: E3 527 SER cc_start: 0.8989 (m) cc_final: 0.8674 (p) REVERT: E3 568 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: E3 570 ASP cc_start: 0.8647 (t0) cc_final: 0.8400 (t0) REVERT: E4 127 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: E4 354 LEU cc_start: 0.8665 (tt) cc_final: 0.8363 (pp) REVERT: E4 453 MET cc_start: 0.9096 (ttt) cc_final: 0.8892 (ttm) outliers start: 64 outliers final: 21 residues processed: 325 average time/residue: 0.7718 time to fit residues: 289.8029 Evaluate side-chains 292 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D5 residue 5 MET Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 39 VAL Chi-restraints excluded: chain D8 residue 70 VAL Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain E1 residue 485 MET Chi-restraints excluded: chain E1 residue 490 VAL Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 112 LEU Chi-restraints excluded: chain E2 residue 290 TYR Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E2 residue 404 GLU Chi-restraints excluded: chain E2 residue 453 MET Chi-restraints excluded: chain E2 residue 483 ASN Chi-restraints excluded: chain E3 residue 485 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E3 residue 568 GLU Chi-restraints excluded: chain E4 residue 127 GLU Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 215 optimal weight: 5.9990 chunk 246 optimal weight: 0.0770 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1 162 GLN D2 112 GLN D3 154 GLN D4 45 ASN D7 171 ASN ** E2 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070110 restraints weight = 54617.377| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.85 r_work: 0.2774 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29070 Z= 0.107 Angle : 0.542 10.194 39512 Z= 0.277 Chirality : 0.041 0.224 4476 Planarity : 0.003 0.040 4733 Dihedral : 12.214 77.761 4958 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.81 % Allowed : 15.23 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.19 (0.14), residues: 3266 helix: 2.51 (0.15), residues: 1076 sheet: 1.24 (0.19), residues: 696 loop : -0.77 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 117 TYR 0.022 0.001 TYRE3 482 PHE 0.025 0.001 PHED7 167 TRP 0.011 0.001 TRPE4 478 HIS 0.003 0.001 HISD1 119 Details of bonding type rmsd covalent geometry : bond 0.00233 (29026) covalent geometry : angle 0.52380 (39464) hydrogen bonds : bond 0.03389 ( 1264) hydrogen bonds : angle 4.12949 ( 3650) metal coordination : bond 0.00499 ( 44) metal coordination : angle 4.07878 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ARG cc_start: 0.9245 (ttp-170) cc_final: 0.8889 (mtm-85) REVERT: D1 9 TYR cc_start: 0.8920 (m-80) cc_final: 0.8551 (m-80) REVERT: D1 12 MET cc_start: 0.9087 (ttp) cc_final: 0.8803 (ttp) REVERT: D1 156 LYS cc_start: 0.8122 (mppt) cc_final: 0.7758 (ttmm) REVERT: D1 157 ASP cc_start: 0.8540 (m-30) cc_final: 0.8328 (m-30) REVERT: D1 171 ASN cc_start: 0.9267 (t0) cc_final: 0.9054 (t0) REVERT: D2 5 MET cc_start: 0.8866 (mtm) cc_final: 0.8425 (mtm) REVERT: D2 102 ASP cc_start: 0.8796 (m-30) cc_final: 0.8595 (m-30) REVERT: D2 108 ASP cc_start: 0.8874 (m-30) cc_final: 0.8615 (m-30) REVERT: D2 112 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: D3 62 MET cc_start: 0.9149 (mtm) cc_final: 0.8831 (mtm) REVERT: D3 69 ASN cc_start: 0.8995 (p0) cc_final: 0.8590 (p0) REVERT: D3 156 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8518 (mtpt) REVERT: D4 34 ARG cc_start: 0.7700 (mpp-170) cc_final: 0.7500 (mpp80) REVERT: D4 125 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: D5 5 MET cc_start: 0.8445 (mtm) cc_final: 0.7923 (mtp) REVERT: D6 154 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: D6 171 ASN cc_start: 0.8420 (m-40) cc_final: 0.8142 (m110) REVERT: D7 29 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: D8 79 ARG cc_start: 0.5889 (tpp-160) cc_final: 0.5233 (mmp-170) REVERT: D8 83 ARG cc_start: 0.6529 (tpm170) cc_final: 0.6264 (tpm170) REVERT: D8 136 GLU cc_start: 0.6383 (mt-10) cc_final: 0.6173 (mp0) REVERT: D8 166 LYS cc_start: 0.8483 (mttt) cc_final: 0.7860 (pttp) REVERT: E1 436 VAL cc_start: 0.8711 (t) cc_final: 0.8324 (m) REVERT: E1 465 ARG cc_start: 0.6866 (mtm110) cc_final: 0.5933 (pmm-80) REVERT: E1 485 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8949 (tmm) REVERT: E1 508 MET cc_start: 0.5649 (ptm) cc_final: 0.5377 (ptm) REVERT: E1 609 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8103 (tp) REVERT: E2 28 ASP cc_start: 0.8113 (m-30) cc_final: 0.7701 (t0) REVERT: E2 33 GLN cc_start: 0.7742 (mm110) cc_final: 0.7325 (tp40) REVERT: E2 47 LYS cc_start: 0.9287 (tttt) cc_final: 0.8793 (ptmm) REVERT: E2 184 MET cc_start: 0.8380 (ptp) cc_final: 0.7706 (mtm) REVERT: E2 230 PHE cc_start: 0.8400 (t80) cc_final: 0.7361 (t80) REVERT: E2 272 LEU cc_start: 0.8273 (mm) cc_final: 0.7927 (mm) REVERT: E2 290 TYR cc_start: 0.6672 (p90) cc_final: 0.6238 (p90) REVERT: E2 297 ASN cc_start: 0.7985 (m-40) cc_final: 0.7727 (p0) REVERT: E2 367 LEU cc_start: 0.7507 (tt) cc_final: 0.7001 (tt) REVERT: E2 368 ASN cc_start: 0.7856 (m-40) cc_final: 0.6970 (t0) REVERT: E2 453 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7993 (ttm) REVERT: E2 480 GLU cc_start: 0.8437 (tp30) cc_final: 0.8192 (tp30) REVERT: E2 503 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6807 (mpp) REVERT: E3 470 ASP cc_start: 0.8629 (p0) cc_final: 0.8220 (p0) REVERT: E3 486 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7043 (mtm110) REVERT: E3 488 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8121 (OUTLIER) REVERT: E3 522 ASN cc_start: 0.9034 (m-40) cc_final: 0.8729 (m-40) REVERT: E3 527 SER cc_start: 0.8917 (m) cc_final: 0.8564 (p) REVERT: E3 568 GLU cc_start: 0.8365 (tp30) cc_final: 0.8090 (tt0) REVERT: E4 127 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: E4 354 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8374 (pp) REVERT: E4 453 MET cc_start: 0.9085 (ttt) cc_final: 0.8845 (ttm) outliers start: 53 outliers final: 19 residues processed: 318 average time/residue: 0.7509 time to fit residues: 276.5888 Evaluate side-chains 293 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 112 GLN Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 108 ASP Chi-restraints excluded: chain D3 residue 123 GLU Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 70 VAL Chi-restraints excluded: chain D8 residue 149 THR Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain E1 residue 485 MET Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 29 CYS Chi-restraints excluded: chain E2 residue 211 LEU Chi-restraints excluded: chain E2 residue 453 MET Chi-restraints excluded: chain E2 residue 503 MET Chi-restraints excluded: chain E3 residue 488 GLN Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 127 GLU Chi-restraints excluded: chain E4 residue 354 LEU Chi-restraints excluded: chain E4 residue 430 LEU Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 252 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1 162 GLN D2 112 GLN D7 171 ASN E2 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067384 restraints weight = 54464.072| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.05 r_work: 0.2759 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29070 Z= 0.143 Angle : 0.553 9.077 39512 Z= 0.282 Chirality : 0.041 0.230 4476 Planarity : 0.003 0.043 4733 Dihedral : 12.136 77.716 4958 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 15.77 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.19 (0.14), residues: 3266 helix: 2.53 (0.15), residues: 1078 sheet: 1.30 (0.19), residues: 673 loop : -0.79 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGD8 40 TYR 0.016 0.001 TYRE1 482 PHE 0.028 0.001 PHED7 167 TRP 0.010 0.001 TRPE3 478 HIS 0.003 0.001 HISE4 62 Details of bonding type rmsd covalent geometry : bond 0.00325 (29026) covalent geometry : angle 0.53719 (39464) hydrogen bonds : bond 0.03469 ( 1264) hydrogen bonds : angle 4.12641 ( 3650) metal coordination : bond 0.00578 ( 44) metal coordination : angle 3.80619 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8904 (tmm-80) cc_final: 0.8701 (tmm-80) REVERT: C 136 ARG cc_start: 0.9255 (ttp-170) cc_final: 0.8848 (mtm-85) REVERT: D1 12 MET cc_start: 0.9065 (ttp) cc_final: 0.8828 (ttp) REVERT: D1 102 ASP cc_start: 0.8872 (t0) cc_final: 0.8610 (t0) REVERT: D1 149 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8747 (t) REVERT: D1 157 ASP cc_start: 0.8582 (m-30) cc_final: 0.8333 (m-30) REVERT: D1 187 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8296 (mm-30) REVERT: D2 5 MET cc_start: 0.8859 (mtm) cc_final: 0.8425 (mtm) REVERT: D2 108 ASP cc_start: 0.8832 (m-30) cc_final: 0.8117 (t0) REVERT: D2 112 GLN cc_start: 0.8810 (mt0) cc_final: 0.8222 (mt0) REVERT: D3 62 MET cc_start: 0.9158 (mtm) cc_final: 0.8805 (mtm) REVERT: D3 69 ASN cc_start: 0.8968 (p0) cc_final: 0.8569 (p0) REVERT: D3 156 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (mtpt) REVERT: D4 69 ASN cc_start: 0.8972 (p0) cc_final: 0.8772 (p0) REVERT: D4 125 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (tp40) REVERT: D5 5 MET cc_start: 0.8469 (mtm) cc_final: 0.7981 (mtp) REVERT: D6 154 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: D6 171 ASN cc_start: 0.8505 (m-40) cc_final: 0.8146 (m110) REVERT: D7 24 ARG cc_start: 0.3751 (OUTLIER) cc_final: 0.3404 (tpp80) REVERT: D7 29 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5727 (mp0) REVERT: D8 79 ARG cc_start: 0.5895 (tpp-160) cc_final: 0.5191 (mmp-170) REVERT: D8 166 LYS cc_start: 0.8397 (mttt) cc_final: 0.8101 (pttp) REVERT: E1 436 VAL cc_start: 0.8597 (t) cc_final: 0.8179 (m) REVERT: E1 465 ARG cc_start: 0.7048 (mtm110) cc_final: 0.6222 (pmm-80) REVERT: E1 485 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8973 (tmm) REVERT: E1 508 MET cc_start: 0.5849 (ptm) cc_final: 0.5593 (ptm) REVERT: E1 592 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8008 (ptmt) REVERT: E1 609 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (tp) REVERT: E2 28 ASP cc_start: 0.8184 (m-30) cc_final: 0.7691 (t0) REVERT: E2 33 GLN cc_start: 0.7822 (mm110) cc_final: 0.7563 (tm-30) REVERT: E2 47 LYS cc_start: 0.9300 (tttt) cc_final: 0.8935 (ptmt) REVERT: E2 184 MET cc_start: 0.8392 (ptp) cc_final: 0.7700 (mtm) REVERT: E2 230 PHE cc_start: 0.8410 (t80) cc_final: 0.7424 (t80) REVERT: E2 272 LEU cc_start: 0.8180 (mm) cc_final: 0.7813 (mm) REVERT: E2 290 TYR cc_start: 0.6593 (p90) cc_final: 0.6140 (p90) REVERT: E2 297 ASN cc_start: 0.7892 (m-40) cc_final: 0.7655 (p0) REVERT: E2 367 LEU cc_start: 0.7409 (tt) cc_final: 0.6455 (tt) REVERT: E2 368 ASN cc_start: 0.8021 (m-40) cc_final: 0.6945 (t0) REVERT: E2 480 GLU cc_start: 0.8463 (tp30) cc_final: 0.8227 (tp30) REVERT: E2 503 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7027 (mpp) REVERT: E3 470 ASP cc_start: 0.8626 (p0) cc_final: 0.8218 (p0) REVERT: E3 486 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6891 (mtm110) REVERT: E3 522 ASN cc_start: 0.9019 (m-40) cc_final: 0.8710 (m-40) REVERT: E3 527 SER cc_start: 0.8961 (m) cc_final: 0.8631 (p) REVERT: E3 568 GLU cc_start: 0.8337 (tp30) cc_final: 0.8116 (tt0) REVERT: E4 354 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8357 (pp) REVERT: E4 453 MET cc_start: 0.9085 (ttt) cc_final: 0.8869 (ttm) outliers start: 52 outliers final: 23 residues processed: 301 average time/residue: 0.7517 time to fit residues: 260.7524 Evaluate side-chains 289 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 149 THR Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 102 ASP Chi-restraints excluded: chain D3 residue 108 ASP Chi-restraints excluded: chain D3 residue 123 GLU Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 108 ASP Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 5 MET Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 24 ARG Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 70 VAL Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain D8 residue 193 VAL Chi-restraints excluded: chain E1 residue 485 MET Chi-restraints excluded: chain E1 residue 592 LYS Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 112 LEU Chi-restraints excluded: chain E2 residue 503 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 354 LEU Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 223 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 311 optimal weight: 0.9990 chunk 287 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 269 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068075 restraints weight = 54526.035| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.03 r_work: 0.2781 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29070 Z= 0.113 Angle : 0.552 13.130 39512 Z= 0.281 Chirality : 0.040 0.225 4476 Planarity : 0.003 0.042 4733 Dihedral : 12.139 77.651 4958 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % Rotamer: Outliers : 1.84 % Allowed : 16.08 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.25 (0.14), residues: 3266 helix: 2.60 (0.15), residues: 1078 sheet: 1.31 (0.20), residues: 659 loop : -0.74 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGD2 83 TYR 0.008 0.001 TYRE2 450 PHE 0.028 0.001 PHEE2 370 TRP 0.009 0.001 TRPE3 478 HIS 0.002 0.001 HISD1 119 Details of bonding type rmsd covalent geometry : bond 0.00250 (29026) covalent geometry : angle 0.53356 (39464) hydrogen bonds : bond 0.03221 ( 1264) hydrogen bonds : angle 4.01842 ( 3650) metal coordination : bond 0.00554 ( 44) metal coordination : angle 4.07847 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ARG cc_start: 0.9261 (ttp-170) cc_final: 0.8910 (ttm110) REVERT: D1 9 TYR cc_start: 0.8873 (m-80) cc_final: 0.8558 (m-80) REVERT: D1 12 MET cc_start: 0.9091 (ttp) cc_final: 0.8820 (ttp) REVERT: D1 102 ASP cc_start: 0.8869 (t0) cc_final: 0.8626 (t0) REVERT: D1 149 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8739 (t) REVERT: D1 156 LYS cc_start: 0.8143 (mppt) cc_final: 0.7875 (tppt) REVERT: D2 5 MET cc_start: 0.8855 (mtm) cc_final: 0.8421 (mtm) REVERT: D2 108 ASP cc_start: 0.8791 (m-30) cc_final: 0.8236 (m-30) REVERT: D2 112 GLN cc_start: 0.8906 (mt0) cc_final: 0.8537 (mt0) REVERT: D2 157 ASP cc_start: 0.8533 (m-30) cc_final: 0.8287 (m-30) REVERT: D3 69 ASN cc_start: 0.8962 (p0) cc_final: 0.8582 (p0) REVERT: D3 156 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8418 (mtpm) REVERT: D4 69 ASN cc_start: 0.9015 (p0) cc_final: 0.8810 (p0) REVERT: D4 125 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8427 (tp40) REVERT: D6 154 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: D6 171 ASN cc_start: 0.8506 (m-40) cc_final: 0.8198 (m110) REVERT: D7 24 ARG cc_start: 0.3776 (OUTLIER) cc_final: 0.3429 (tpp80) REVERT: D7 29 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5758 (mp0) REVERT: D7 87 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5875 (m) REVERT: D7 136 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6626 (mt-10) REVERT: D8 77 ARG cc_start: 0.3780 (ttm170) cc_final: 0.3484 (mtt180) REVERT: D8 79 ARG cc_start: 0.5061 (tpp-160) cc_final: 0.4420 (mmp-170) REVERT: D8 166 LYS cc_start: 0.8369 (mttt) cc_final: 0.8068 (pptt) REVERT: E1 436 VAL cc_start: 0.8622 (t) cc_final: 0.8260 (m) REVERT: E1 465 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6395 (pmm-80) REVERT: E1 485 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8981 (tmm) REVERT: E1 508 MET cc_start: 0.5928 (ptm) cc_final: 0.5698 (ptm) REVERT: E1 592 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7963 (ptmt) REVERT: E1 609 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8075 (tp) REVERT: E2 28 ASP cc_start: 0.8248 (m-30) cc_final: 0.7761 (t0) REVERT: E2 33 GLN cc_start: 0.7880 (mm110) cc_final: 0.7491 (tm-30) REVERT: E2 47 LYS cc_start: 0.9314 (tttt) cc_final: 0.8955 (ptmt) REVERT: E2 184 MET cc_start: 0.8368 (ptp) cc_final: 0.7673 (mtm) REVERT: E2 230 PHE cc_start: 0.8414 (t80) cc_final: 0.7413 (t80) REVERT: E2 272 LEU cc_start: 0.8214 (mm) cc_final: 0.7858 (mm) REVERT: E2 286 PHE cc_start: 0.7195 (m-80) cc_final: 0.6809 (m-80) REVERT: E2 290 TYR cc_start: 0.6650 (p90) cc_final: 0.6235 (p90) REVERT: E2 297 ASN cc_start: 0.7985 (m-40) cc_final: 0.7752 (p0) REVERT: E2 367 LEU cc_start: 0.7800 (tt) cc_final: 0.7195 (tt) REVERT: E2 368 ASN cc_start: 0.8080 (m-40) cc_final: 0.7084 (t0) REVERT: E2 402 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: E2 444 MET cc_start: 0.9216 (mmm) cc_final: 0.8246 (tpp) REVERT: E2 480 GLU cc_start: 0.8482 (tp30) cc_final: 0.8227 (tp30) REVERT: E2 503 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6970 (mpp) REVERT: E3 470 ASP cc_start: 0.8631 (p0) cc_final: 0.8230 (p0) REVERT: E3 482 TYR cc_start: 0.8448 (t80) cc_final: 0.8243 (t80) REVERT: E3 522 ASN cc_start: 0.9014 (m-40) cc_final: 0.8711 (m-40) REVERT: E3 527 SER cc_start: 0.8959 (m) cc_final: 0.8585 (p) REVERT: E3 554 ARG cc_start: 0.8727 (ttt90) cc_final: 0.8447 (ttm-80) REVERT: E3 568 GLU cc_start: 0.8407 (tp30) cc_final: 0.8115 (tt0) REVERT: E4 453 MET cc_start: 0.9060 (ttt) cc_final: 0.8853 (ttm) REVERT: E4 465 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7778 (ptm160) outliers start: 54 outliers final: 25 residues processed: 304 average time/residue: 0.7780 time to fit residues: 272.5750 Evaluate side-chains 283 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 149 THR Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 20 THR Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 108 ASP Chi-restraints excluded: chain D3 residue 123 GLU Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 108 ASP Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 24 ARG Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 87 CYS Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 138 VAL Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain D8 residue 193 VAL Chi-restraints excluded: chain E1 residue 485 MET Chi-restraints excluded: chain E1 residue 592 LYS Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 112 LEU Chi-restraints excluded: chain E2 residue 211 LEU Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E2 residue 503 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 430 LEU Chi-restraints excluded: chain E4 residue 439 ILE Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 10 optimal weight: 0.1980 chunk 177 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D7 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.066394 restraints weight = 54704.756| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.77 r_work: 0.2736 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29070 Z= 0.192 Angle : 0.597 11.931 39512 Z= 0.300 Chirality : 0.042 0.238 4476 Planarity : 0.003 0.039 4733 Dihedral : 12.077 77.826 4958 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.64 % Allowed : 16.46 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.21 (0.14), residues: 3266 helix: 2.64 (0.15), residues: 1072 sheet: 1.23 (0.20), residues: 669 loop : -0.79 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGD8 40 TYR 0.017 0.001 TYRE1 482 PHE 0.020 0.001 PHEE2 286 TRP 0.008 0.001 TRPE3 478 HIS 0.004 0.001 HISE4 62 Details of bonding type rmsd covalent geometry : bond 0.00442 (29026) covalent geometry : angle 0.57874 (39464) hydrogen bonds : bond 0.03683 ( 1264) hydrogen bonds : angle 4.11878 ( 3650) metal coordination : bond 0.00852 ( 44) metal coordination : angle 4.23538 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ARG cc_start: 0.9251 (ttp-170) cc_final: 0.8850 (mtm-85) REVERT: D1 12 MET cc_start: 0.9088 (ttp) cc_final: 0.8801 (ttp) REVERT: D1 102 ASP cc_start: 0.8829 (t0) cc_final: 0.8569 (t0) REVERT: D1 149 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8764 (t) REVERT: D2 5 MET cc_start: 0.8876 (mtm) cc_final: 0.8472 (mtm) REVERT: D2 157 ASP cc_start: 0.8559 (m-30) cc_final: 0.8235 (m-30) REVERT: D3 62 MET cc_start: 0.9136 (mtm) cc_final: 0.8833 (mtm) REVERT: D3 69 ASN cc_start: 0.8941 (p0) cc_final: 0.8545 (p0) REVERT: D3 110 LYS cc_start: 0.9045 (pttp) cc_final: 0.8783 (ptpp) REVERT: D3 156 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (mtpt) REVERT: D4 125 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8436 (tp40) REVERT: D6 154 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: D7 24 ARG cc_start: 0.4193 (OUTLIER) cc_final: 0.3790 (tpp80) REVERT: D7 29 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5656 (mp0) REVERT: D7 72 ASP cc_start: 0.8137 (p0) cc_final: 0.7651 (t70) REVERT: D7 87 CYS cc_start: 0.6276 (OUTLIER) cc_final: 0.6015 (m) REVERT: D7 136 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6916 (mt-10) REVERT: D8 79 ARG cc_start: 0.5476 (tpp-160) cc_final: 0.4832 (mmp-170) REVERT: D8 166 LYS cc_start: 0.8407 (mttt) cc_final: 0.8036 (pptt) REVERT: E1 436 VAL cc_start: 0.8650 (t) cc_final: 0.8227 (m) REVERT: E1 465 ARG cc_start: 0.7303 (mtm110) cc_final: 0.6509 (pmm-80) REVERT: E1 485 MET cc_start: 0.9174 (tmm) cc_final: 0.8953 (tmm) REVERT: E1 592 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (ptmt) REVERT: E1 609 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8110 (tp) REVERT: E2 28 ASP cc_start: 0.8228 (m-30) cc_final: 0.7840 (t0) REVERT: E2 33 GLN cc_start: 0.7866 (mm110) cc_final: 0.7540 (tm-30) REVERT: E2 47 LYS cc_start: 0.9318 (tttt) cc_final: 0.8957 (ptmt) REVERT: E2 184 MET cc_start: 0.8396 (ptp) cc_final: 0.7676 (mtm) REVERT: E2 230 PHE cc_start: 0.8424 (t80) cc_final: 0.7428 (t80) REVERT: E2 272 LEU cc_start: 0.8340 (mm) cc_final: 0.7954 (mm) REVERT: E2 286 PHE cc_start: 0.7329 (m-80) cc_final: 0.6918 (m-80) REVERT: E2 290 TYR cc_start: 0.6401 (p90) cc_final: 0.6010 (p90) REVERT: E2 297 ASN cc_start: 0.7944 (m-40) cc_final: 0.7685 (p0) REVERT: E2 367 LEU cc_start: 0.7885 (tt) cc_final: 0.7479 (tt) REVERT: E2 368 ASN cc_start: 0.8129 (m-40) cc_final: 0.7205 (t0) REVERT: E2 480 GLU cc_start: 0.8478 (tp30) cc_final: 0.8226 (tp30) REVERT: E2 483 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: E2 503 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7043 (mpp) REVERT: E3 470 ASP cc_start: 0.8664 (p0) cc_final: 0.8239 (p0) REVERT: E3 486 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6788 (mtm110) REVERT: E3 522 ASN cc_start: 0.9017 (m-40) cc_final: 0.8713 (m-40) REVERT: E3 527 SER cc_start: 0.9009 (m) cc_final: 0.8705 (p) REVERT: E3 554 ARG cc_start: 0.8733 (ttt90) cc_final: 0.8481 (ttm-80) REVERT: E3 568 GLU cc_start: 0.8385 (tp30) cc_final: 0.8087 (tt0) REVERT: E4 453 MET cc_start: 0.9103 (ttt) cc_final: 0.8892 (ttm) REVERT: E4 465 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7808 (ptm160) outliers start: 48 outliers final: 24 residues processed: 299 average time/residue: 0.7843 time to fit residues: 270.4068 Evaluate side-chains 292 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 149 THR Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 20 THR Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 102 ASP Chi-restraints excluded: chain D3 residue 108 ASP Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 108 ASP Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 24 ARG Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 87 CYS Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain D8 residue 193 VAL Chi-restraints excluded: chain E1 residue 490 VAL Chi-restraints excluded: chain E1 residue 592 LYS Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 17 LEU Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E2 residue 483 ASN Chi-restraints excluded: chain E2 residue 503 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 290 optimal weight: 0.4980 chunk 164 optimal weight: 20.0000 chunk 323 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D2 112 GLN D3 154 GLN D7 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070173 restraints weight = 54669.767| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.86 r_work: 0.2765 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29070 Z= 0.111 Angle : 0.574 11.978 39512 Z= 0.289 Chirality : 0.041 0.225 4476 Planarity : 0.003 0.043 4733 Dihedral : 12.149 77.745 4958 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 16.56 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.25 (0.14), residues: 3266 helix: 2.65 (0.15), residues: 1072 sheet: 1.21 (0.20), residues: 671 loop : -0.73 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGD4 34 TYR 0.007 0.001 TYRE2 115 PHE 0.017 0.001 PHEE2 286 TRP 0.009 0.001 TRPE3 478 HIS 0.003 0.001 HISD1 119 Details of bonding type rmsd covalent geometry : bond 0.00245 (29026) covalent geometry : angle 0.55575 (39464) hydrogen bonds : bond 0.03216 ( 1264) hydrogen bonds : angle 3.97088 ( 3650) metal coordination : bond 0.00488 ( 44) metal coordination : angle 4.14025 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 9 TYR cc_start: 0.8868 (m-80) cc_final: 0.8533 (m-80) REVERT: D1 12 MET cc_start: 0.9098 (ttp) cc_final: 0.8832 (ttp) REVERT: D1 102 ASP cc_start: 0.8852 (t0) cc_final: 0.8599 (t0) REVERT: D1 149 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8723 (t) REVERT: D1 156 LYS cc_start: 0.8176 (mppt) cc_final: 0.7831 (tppt) REVERT: D1 162 GLN cc_start: 0.9206 (mt0) cc_final: 0.8920 (mt0) REVERT: D2 5 MET cc_start: 0.8828 (mtm) cc_final: 0.8394 (mtm) REVERT: D2 108 ASP cc_start: 0.8827 (m-30) cc_final: 0.8025 (t0) REVERT: D2 112 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: D2 157 ASP cc_start: 0.8532 (m-30) cc_final: 0.8258 (m-30) REVERT: D3 62 MET cc_start: 0.9029 (mtm) cc_final: 0.8783 (mtm) REVERT: D3 69 ASN cc_start: 0.8996 (p0) cc_final: 0.8636 (p0) REVERT: D3 156 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8429 (mtpm) REVERT: D4 34 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7595 (mpp80) REVERT: D4 125 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8427 (tp40) REVERT: D6 154 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: D7 24 ARG cc_start: 0.3990 (OUTLIER) cc_final: 0.3612 (tpp80) REVERT: D7 29 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5607 (mp0) REVERT: D7 87 CYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5994 (m) REVERT: D8 6 LYS cc_start: 0.4276 (mppt) cc_final: 0.3426 (mttp) REVERT: D8 77 ARG cc_start: 0.3204 (ttm170) cc_final: 0.2858 (ttt180) REVERT: D8 79 ARG cc_start: 0.5159 (tpp-160) cc_final: 0.4413 (mmp-170) REVERT: D8 166 LYS cc_start: 0.8390 (mttt) cc_final: 0.8053 (pptt) REVERT: E1 436 VAL cc_start: 0.8726 (t) cc_final: 0.8371 (m) REVERT: E1 465 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6543 (pmm-80) REVERT: E1 485 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8974 (tmm) REVERT: E1 508 MET cc_start: 0.5913 (ptm) cc_final: 0.5576 (ptm) REVERT: E1 511 ASP cc_start: 0.9246 (m-30) cc_final: 0.9041 (p0) REVERT: E1 592 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8098 (ptmt) REVERT: E1 609 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (tp) REVERT: E2 28 ASP cc_start: 0.8148 (m-30) cc_final: 0.7762 (t0) REVERT: E2 33 GLN cc_start: 0.7911 (mm110) cc_final: 0.7548 (tm-30) REVERT: E2 47 LYS cc_start: 0.9304 (tttt) cc_final: 0.8861 (ptmm) REVERT: E2 184 MET cc_start: 0.8387 (ptp) cc_final: 0.7684 (mtm) REVERT: E2 230 PHE cc_start: 0.8401 (t80) cc_final: 0.7378 (t80) REVERT: E2 272 LEU cc_start: 0.8393 (mm) cc_final: 0.8026 (mm) REVERT: E2 286 PHE cc_start: 0.7309 (m-80) cc_final: 0.6881 (m-80) REVERT: E2 290 TYR cc_start: 0.6470 (p90) cc_final: 0.6101 (p90) REVERT: E2 297 ASN cc_start: 0.7897 (m-40) cc_final: 0.7621 (p0) REVERT: E2 367 LEU cc_start: 0.8062 (tt) cc_final: 0.7666 (tt) REVERT: E2 368 ASN cc_start: 0.8210 (m-40) cc_final: 0.7459 (t0) REVERT: E2 402 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: E2 480 GLU cc_start: 0.8478 (tp30) cc_final: 0.8209 (tp30) REVERT: E2 503 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7050 (mpp) REVERT: E3 470 ASP cc_start: 0.8681 (p0) cc_final: 0.8242 (p0) REVERT: E3 522 ASN cc_start: 0.9018 (m-40) cc_final: 0.8714 (m-40) REVERT: E3 554 ARG cc_start: 0.8771 (ttt90) cc_final: 0.8484 (ttm-80) REVERT: E3 568 GLU cc_start: 0.8429 (tp30) cc_final: 0.8147 (tt0) REVERT: E4 453 MET cc_start: 0.9066 (ttt) cc_final: 0.8850 (ttm) REVERT: E4 465 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7813 (ptm160) outliers start: 48 outliers final: 23 residues processed: 292 average time/residue: 0.7760 time to fit residues: 261.0386 Evaluate side-chains 287 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 149 THR Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 20 THR Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D2 residue 112 GLN Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 108 ASP Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 108 ASP Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 24 ARG Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 87 CYS Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 138 VAL Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain E1 residue 485 MET Chi-restraints excluded: chain E1 residue 490 VAL Chi-restraints excluded: chain E1 residue 509 SER Chi-restraints excluded: chain E1 residue 592 LYS Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 17 LEU Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E2 residue 503 MET Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 252 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 206 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1 125 GLN D2 112 GLN D4 69 ASN E2 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.111630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070272 restraints weight = 54293.928| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.90 r_work: 0.2784 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29070 Z= 0.111 Angle : 0.590 14.005 39512 Z= 0.294 Chirality : 0.040 0.222 4476 Planarity : 0.003 0.037 4733 Dihedral : 12.137 77.756 4958 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 16.97 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.27 (0.14), residues: 3266 helix: 2.67 (0.15), residues: 1073 sheet: 1.22 (0.20), residues: 671 loop : -0.72 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGD4 34 TYR 0.023 0.001 TYRE1 482 PHE 0.017 0.001 PHEE2 286 TRP 0.008 0.001 TRPE3 478 HIS 0.002 0.001 HISD1 119 Details of bonding type rmsd covalent geometry : bond 0.00248 (29026) covalent geometry : angle 0.57222 (39464) hydrogen bonds : bond 0.03154 ( 1264) hydrogen bonds : angle 3.94729 ( 3650) metal coordination : bond 0.00487 ( 44) metal coordination : angle 4.13795 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 9 TYR cc_start: 0.8913 (m-80) cc_final: 0.8625 (m-80) REVERT: D1 12 MET cc_start: 0.9045 (ttp) cc_final: 0.8781 (ttp) REVERT: D1 102 ASP cc_start: 0.8810 (t0) cc_final: 0.8587 (t0) REVERT: D1 149 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8737 (t) REVERT: D2 5 MET cc_start: 0.8867 (mtm) cc_final: 0.8400 (mtm) REVERT: D2 157 ASP cc_start: 0.8540 (m-30) cc_final: 0.8302 (m-30) REVERT: D3 62 MET cc_start: 0.9068 (mtm) cc_final: 0.8866 (mtm) REVERT: D3 69 ASN cc_start: 0.8960 (p0) cc_final: 0.8609 (p0) REVERT: D3 156 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8464 (mtpm) REVERT: D4 34 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7568 (mpp80) REVERT: D4 125 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8417 (tp40) REVERT: D6 154 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: D7 24 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.4065 (tpp80) REVERT: D7 29 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5809 (mp0) REVERT: D7 87 CYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6133 (m) REVERT: D8 62 MET cc_start: 0.4735 (mmt) cc_final: 0.4491 (mpt) REVERT: D8 77 ARG cc_start: 0.3354 (ttm170) cc_final: 0.2999 (ttt180) REVERT: D8 79 ARG cc_start: 0.5152 (tpp-160) cc_final: 0.4380 (mmp-170) REVERT: D8 166 LYS cc_start: 0.8454 (mttt) cc_final: 0.8115 (pptt) REVERT: E1 436 VAL cc_start: 0.8815 (t) cc_final: 0.8489 (m) REVERT: E1 465 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6548 (pmm-80) REVERT: E1 485 MET cc_start: 0.9208 (tmm) cc_final: 0.9007 (tmm) REVERT: E1 508 MET cc_start: 0.6248 (ptm) cc_final: 0.5925 (ptm) REVERT: E1 592 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (ptmt) REVERT: E1 609 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8043 (tp) REVERT: E2 28 ASP cc_start: 0.8093 (m-30) cc_final: 0.7797 (t0) REVERT: E2 33 GLN cc_start: 0.7936 (mm110) cc_final: 0.7575 (tm-30) REVERT: E2 47 LYS cc_start: 0.9267 (tttt) cc_final: 0.8843 (ptmm) REVERT: E2 184 MET cc_start: 0.8366 (ptp) cc_final: 0.7856 (mtm) REVERT: E2 230 PHE cc_start: 0.8322 (t80) cc_final: 0.7365 (t80) REVERT: E2 272 LEU cc_start: 0.8425 (mm) cc_final: 0.8031 (mm) REVERT: E2 290 TYR cc_start: 0.6474 (p90) cc_final: 0.6087 (p90) REVERT: E2 297 ASN cc_start: 0.7935 (m-40) cc_final: 0.7654 (p0) REVERT: E2 367 LEU cc_start: 0.7959 (tt) cc_final: 0.7654 (tt) REVERT: E2 368 ASN cc_start: 0.8198 (m-40) cc_final: 0.7553 (t0) REVERT: E2 402 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: E2 480 GLU cc_start: 0.8450 (tp30) cc_final: 0.8182 (tp30) REVERT: E2 503 MET cc_start: 0.7179 (mpt) cc_final: 0.6961 (mpp) REVERT: E3 470 ASP cc_start: 0.8724 (p0) cc_final: 0.8286 (p0) REVERT: E3 482 TYR cc_start: 0.8444 (t80) cc_final: 0.8232 (t80) REVERT: E3 522 ASN cc_start: 0.9002 (m-40) cc_final: 0.8727 (m-40) REVERT: E3 554 ARG cc_start: 0.8763 (ttt90) cc_final: 0.8512 (ttm-80) REVERT: E3 568 GLU cc_start: 0.8396 (tp30) cc_final: 0.8154 (tt0) REVERT: E4 453 MET cc_start: 0.9128 (ttt) cc_final: 0.8913 (ttm) REVERT: E4 465 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7887 (ptm160) REVERT: E4 478 TRP cc_start: 0.8219 (t60) cc_final: 0.7889 (t60) outliers start: 37 outliers final: 22 residues processed: 282 average time/residue: 0.7636 time to fit residues: 248.7479 Evaluate side-chains 280 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D1 residue 62 MET Chi-restraints excluded: chain D1 residue 140 GLU Chi-restraints excluded: chain D1 residue 149 THR Chi-restraints excluded: chain D1 residue 158 LEU Chi-restraints excluded: chain D2 residue 20 THR Chi-restraints excluded: chain D2 residue 39 VAL Chi-restraints excluded: chain D2 residue 187 GLU Chi-restraints excluded: chain D3 residue 156 LYS Chi-restraints excluded: chain D4 residue 108 ASP Chi-restraints excluded: chain D4 residue 125 GLN Chi-restraints excluded: chain D5 residue 32 GLN Chi-restraints excluded: chain D6 residue 154 GLN Chi-restraints excluded: chain D6 residue 192 ASP Chi-restraints excluded: chain D7 residue 24 ARG Chi-restraints excluded: chain D7 residue 29 GLU Chi-restraints excluded: chain D7 residue 44 THR Chi-restraints excluded: chain D7 residue 87 CYS Chi-restraints excluded: chain D7 residue 158 LEU Chi-restraints excluded: chain D7 residue 185 SER Chi-restraints excluded: chain D8 residue 138 VAL Chi-restraints excluded: chain D8 residue 159 SER Chi-restraints excluded: chain E1 residue 490 VAL Chi-restraints excluded: chain E1 residue 592 LYS Chi-restraints excluded: chain E1 residue 609 LEU Chi-restraints excluded: chain E2 residue 9 SER Chi-restraints excluded: chain E2 residue 17 LEU Chi-restraints excluded: chain E2 residue 402 GLN Chi-restraints excluded: chain E3 residue 511 ASP Chi-restraints excluded: chain E4 residue 439 ILE Chi-restraints excluded: chain E4 residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 275 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 307 optimal weight: 0.0470 chunk 293 optimal weight: 0.1980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4 69 ASN E1 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.067898 restraints weight = 54629.085| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.94 r_work: 0.2765 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29070 Z= 0.137 Angle : 0.593 12.039 39512 Z= 0.300 Chirality : 0.041 0.228 4476 Planarity : 0.003 0.048 4733 Dihedral : 12.102 77.776 4958 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.37 % Allowed : 17.14 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.06 % 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: 1.24 (0.14), residues: 3266 helix: 2.66 (0.15), residues: 1073 sheet: 1.19 (0.20), residues: 671 loop : -0.75 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGE3 486 TYR 0.019 0.001 TYRE3 482 PHE 0.056 0.001 PHED8 144 TRP 0.007 0.001 TRPE3 478 HIS 0.003 0.001 HISE4 62 Details of bonding type rmsd covalent geometry : bond 0.00311 (29026) covalent geometry : angle 0.57704 (39464) hydrogen bonds : bond 0.03272 ( 1264) hydrogen bonds : angle 3.98729 ( 3650) metal coordination : bond 0.00533 ( 44) metal coordination : angle 3.93839 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10791.29 seconds wall clock time: 184 minutes 17.81 seconds (11057.81 seconds total)