Starting phenix.real_space_refine on Sat Jul 4 21:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl6_45663/07_2026/9cl6_45663.map" } resolution = 2.77 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= 0.006 sd= 0.193 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: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 135 5.16 5 C 15273 2.51 5 N 3780 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23928 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2119 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3039 Classifications: {'peptide': 383} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 354} Chain: "B" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2252 Classifications: {'peptide': 274} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 257} Chain: "Da" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 290 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Da" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "Db" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "Dc" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Restraints were copied for chains: J, G, H, E, I, F, Db, Dc Time building chain proxies: 4.72, per 1000 atoms: 0.20 Number of scatterers: 23928 At special positions: 0 Unit cell: (111.22, 116.2, 127.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 135 16.00 O 4734 8.00 N 3780 7.00 C 15273 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: 1.97 Conformation dependent library (CDL) restraints added in 870.0 milliseconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 21 sheets defined 59.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 26 through 55 removed outlier: 5.843A pdb=" N TYR C 52 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 92 removed outlier: 3.994A pdb=" N GLY C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Proline residue: C 79 - end of helix Processing helix chain 'C' and resid 95 through 101 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 141 removed outlier: 4.514A pdb=" N ASP C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 159 through 179 Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'C' and resid 187 through 201 Proline residue: C 197 - end of helix removed outlier: 3.725A pdb=" N LEU C 201 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 4.227A pdb=" N LEU C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 225 through 233 removed outlier: 4.179A pdb=" N VAL C 229 " --> pdb=" O HIS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 266 removed outlier: 3.717A pdb=" N ILE C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.770A pdb=" N GLY A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.824A pdb=" N MET A 233 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 263 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.646A pdb=" N TYR A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 379 through 386 removed outlier: 3.638A pdb=" N ALA A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 384 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 385 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 16 through 56 Proline residue: B 32 - end of helix removed outlier: 7.277A pdb=" N ASP B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 64 through 89 Proline residue: B 70 - end of helix removed outlier: 4.070A pdb=" N THR B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.878A pdb=" N THR B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 144 removed outlier: 3.845A pdb=" N ALA B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 160 through 170 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.584A pdb=" N VAL B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 244 removed outlier: 3.536A pdb=" N ALA B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 270 through 276 removed outlier: 4.497A pdb=" N LYS B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'Da' and resid 6 through 20 removed outlier: 3.632A pdb=" N SERDa 17 " --> pdb=" O ILEDa 13 " (cutoff:3.500A) Processing helix chain 'Da' and resid 20 through 41 removed outlier: 3.785A pdb=" N LEUDa 24 " --> pdb=" O TRPDa 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SERDa 26 " --> pdb=" O VALDa 22 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALADa 28 " --> pdb=" O LEUDa 24 " (cutoff:3.500A) Processing helix chain 'Db' and resid 6 through 20 removed outlier: 3.631A pdb=" N SERDb 17 " --> pdb=" O ILEDb 13 " (cutoff:3.500A) Processing helix chain 'Db' and resid 20 through 41 removed outlier: 3.785A pdb=" N LEUDb 24 " --> pdb=" O TRPDb 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SERDb 26 " --> pdb=" O VALDb 22 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALADb 28 " --> pdb=" O LEUDb 24 " (cutoff:3.500A) Processing helix chain 'Dc' and resid 6 through 20 removed outlier: 3.631A pdb=" N SERDc 17 " --> pdb=" O ILEDc 13 " (cutoff:3.500A) Processing helix chain 'Dc' and resid 20 through 41 removed outlier: 3.785A pdb=" N LEUDc 24 " --> pdb=" O TRPDc 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SERDc 26 " --> pdb=" O VALDc 22 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALADc 28 " --> pdb=" O LEUDc 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 14 Processing helix chain 'I' and resid 16 through 56 Proline residue: I 32 - end of helix removed outlier: 7.278A pdb=" N ASP I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 60 Processing helix chain 'I' and resid 64 through 89 Proline residue: I 70 - end of helix removed outlier: 4.070A pdb=" N THR I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 112 Processing helix chain 'I' and resid 121 through 125 removed outlier: 3.877A pdb=" N THR I 125 " --> pdb=" O ASN I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 144 removed outlier: 3.845A pdb=" N ALA I 133 " --> pdb=" O MET I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 160 through 170 Proline residue: I 167 - end of helix Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 185 through 193 Processing helix chain 'I' and resid 199 through 203 removed outlier: 3.585A pdb=" N VAL I 202 " --> pdb=" O PRO I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 244 removed outlier: 3.535A pdb=" N ALA I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR I 234 " --> pdb=" O MET I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'I' and resid 270 through 276 removed outlier: 4.497A pdb=" N LYS I 276 " --> pdb=" O PRO I 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 16 through 56 Proline residue: F 32 - end of helix removed outlier: 7.277A pdb=" N ASP F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 64 through 89 Proline residue: F 70 - end of helix removed outlier: 4.071A pdb=" N THR F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 112 Processing helix chain 'F' and resid 121 through 125 removed outlier: 3.878A pdb=" N THR F 125 " --> pdb=" O ASN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 144 removed outlier: 3.845A pdb=" N ALA F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 160 through 170 Proline residue: F 167 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.584A pdb=" N VAL F 202 " --> pdb=" O PRO F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 244 removed outlier: 3.536A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 270 through 276 removed outlier: 4.497A pdb=" N LYS F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 55 removed outlier: 5.843A pdb=" N TYR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 92 removed outlier: 3.994A pdb=" N GLY J 69 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Proline residue: J 79 - end of helix Processing helix chain 'J' and resid 95 through 101 Processing helix chain 'J' and resid 103 through 130 Processing helix chain 'J' and resid 130 through 141 removed outlier: 4.514A pdb=" N ASP J 136 " --> pdb=" O PHE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 159 through 179 Processing helix chain 'J' and resid 179 through 185 Processing helix chain 'J' and resid 187 through 201 Proline residue: J 197 - end of helix removed outlier: 3.725A pdb=" N LEU J 201 " --> pdb=" O PRO J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 213 removed outlier: 4.227A pdb=" N LEU J 206 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 225 through 233 removed outlier: 4.179A pdb=" N VAL J 229 " --> pdb=" O HIS J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 258 Processing helix chain 'J' and resid 261 through 266 removed outlier: 3.717A pdb=" N ILE J 264 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 55 removed outlier: 5.843A pdb=" N TYR G 52 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 92 removed outlier: 3.994A pdb=" N GLY G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 95 through 101 Processing helix chain 'G' and resid 103 through 130 Processing helix chain 'G' and resid 130 through 141 removed outlier: 4.515A pdb=" N ASP G 136 " --> pdb=" O PHE G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 156 removed outlier: 3.500A pdb=" N VAL G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 179 Processing helix chain 'G' and resid 179 through 185 Processing helix chain 'G' and resid 187 through 201 Proline residue: G 197 - end of helix removed outlier: 3.725A pdb=" N LEU G 201 " --> pdb=" O PRO G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 213 removed outlier: 4.227A pdb=" N LEU G 206 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 225 through 233 removed outlier: 4.179A pdb=" N VAL G 229 " --> pdb=" O HIS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 258 Processing helix chain 'G' and resid 261 through 266 removed outlier: 3.716A pdb=" N ILE G 264 " --> pdb=" O SER G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 167 through 171 Processing helix chain 'H' and resid 189 through 210 removed outlier: 3.770A pdb=" N GLY H 193 " --> pdb=" O ASN H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 228 Processing helix chain 'H' and resid 229 through 233 removed outlier: 3.824A pdb=" N MET H 233 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 263 Processing helix chain 'H' and resid 330 through 336 removed outlier: 3.646A pdb=" N TYR H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 344 No H-bonds generated for 'chain 'H' and resid 342 through 344' Processing helix chain 'H' and resid 373 through 378 Processing helix chain 'H' and resid 379 through 386 removed outlier: 3.637A pdb=" N ALA H 382 " --> pdb=" O ARG H 379 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU H 384 " --> pdb=" O MET H 381 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY H 385 " --> pdb=" O ALA H 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP H 386 " --> pdb=" O LEU H 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 189 through 210 removed outlier: 3.770A pdb=" N GLY E 193 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.824A pdb=" N MET E 233 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 263 Processing helix chain 'E' and resid 330 through 336 removed outlier: 3.646A pdb=" N TYR E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 373 through 378 Processing helix chain 'E' and resid 379 through 386 removed outlier: 3.638A pdb=" N ALA E 382 " --> pdb=" O ARG E 379 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 384 " --> pdb=" O MET E 381 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 386 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 60 removed outlier: 4.364A pdb=" N ILE A 57 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A 73 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP A 59 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 71 " --> pdb=" O TRP A 59 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 134 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG A 105 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 removed outlier: 6.521A pdb=" N VAL A 149 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA A 156 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 147 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 145 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 160 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.786A pdb=" N GLN A 362 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 307 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE A 290 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR A 309 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 288 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.284A pdb=" N ARG A 327 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE A 318 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 398 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 178 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.536A pdb=" N ARG B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 175 through 178 Processing sheet with id=AA9, first strand: chain 'I' and resid 248 through 252 removed outlier: 3.537A pdb=" N ARG I 256 " --> pdb=" O GLY I 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB2, first strand: chain 'F' and resid 248 through 252 removed outlier: 3.536A pdb=" N ARG F 256 " --> pdb=" O GLY F 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 52 through 60 removed outlier: 4.363A pdb=" N ILE H 57 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR H 73 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP H 59 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS H 71 " --> pdb=" O TRP H 59 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG H 134 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG H 105 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 63 through 65 removed outlier: 6.521A pdb=" N VAL H 149 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA H 156 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU H 147 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA H 145 " --> pdb=" O PRO H 158 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 160 " --> pdb=" O MET H 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 174 through 176 Processing sheet with id=AB6, first strand: chain 'H' and resid 350 through 352 removed outlier: 3.786A pdb=" N GLN H 362 " --> pdb=" O ASN H 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU H 307 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE H 290 " --> pdb=" O GLU H 307 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR H 309 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE H 288 " --> pdb=" O THR H 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 346 through 347 removed outlier: 6.285A pdb=" N ARG H 327 " --> pdb=" O ALA H 347 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE H 318 " --> pdb=" O TRP H 398 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP H 398 " --> pdb=" O PHE H 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 52 through 60 removed outlier: 4.363A pdb=" N ILE E 57 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR E 73 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP E 59 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 71 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG E 134 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG E 105 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.522A pdb=" N VAL E 149 " --> pdb=" O PRO E 154 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA E 156 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 147 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 145 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA E 160 " --> pdb=" O MET E 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 174 through 176 Processing sheet with id=AC2, first strand: chain 'E' and resid 350 through 352 removed outlier: 3.786A pdb=" N GLN E 362 " --> pdb=" O ASN E 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU E 307 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE E 290 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR E 309 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE E 288 " --> pdb=" O THR E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 346 through 347 removed outlier: 6.284A pdb=" N ARG E 327 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE E 318 " --> pdb=" O TRP E 398 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TRP E 398 " --> pdb=" O PHE E 318 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3492 1.28 - 1.41: 6971 1.41 - 1.55: 13172 1.55 - 1.68: 8 1.68 - 1.81: 255 Bond restraints: 23898 Sorted by residual: bond pdb=" C LYS H 58 " pdb=" O LYS H 58 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.14e-02 7.69e+03 5.18e+01 bond pdb=" C LYS A 58 " pdb=" O LYS A 58 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.14e-02 7.69e+03 5.13e+01 bond pdb=" C LYS E 58 " pdb=" O LYS E 58 " ideal model delta sigma weight residual 1.236 1.154 0.081 1.14e-02 7.69e+03 5.11e+01 bond pdb=" C ALA H 145 " pdb=" O ALA H 145 " ideal model delta sigma weight residual 1.236 1.149 0.086 1.21e-02 6.83e+03 5.08e+01 bond pdb=" C ALA A 145 " pdb=" O ALA A 145 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.21e-02 6.83e+03 5.07e+01 ... (remaining 23893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 30805 1.95 - 3.89: 1472 3.89 - 5.84: 228 5.84 - 7.79: 69 7.79 - 9.73: 12 Bond angle restraints: 32586 Sorted by residual: angle pdb=" N ILEDb 23 " pdb=" CA ILEDb 23 " pdb=" C ILEDb 23 " ideal model delta sigma weight residual 111.81 104.35 7.46 8.60e-01 1.35e+00 7.53e+01 angle pdb=" N ILEDa 23 " pdb=" CA ILEDa 23 " pdb=" C ILEDa 23 " ideal model delta sigma weight residual 111.81 104.37 7.44 8.60e-01 1.35e+00 7.49e+01 angle pdb=" N ILEDc 23 " pdb=" CA ILEDc 23 " pdb=" C ILEDc 23 " ideal model delta sigma weight residual 111.81 104.40 7.41 8.60e-01 1.35e+00 7.41e+01 angle pdb=" CA HIS A 144 " pdb=" CB HIS A 144 " pdb=" CG HIS A 144 " ideal model delta sigma weight residual 113.80 120.76 -6.96 1.00e+00 1.00e+00 4.85e+01 angle pdb=" CA HIS H 144 " pdb=" CB HIS H 144 " pdb=" CG HIS H 144 " ideal model delta sigma weight residual 113.80 120.76 -6.96 1.00e+00 1.00e+00 4.85e+01 ... (remaining 32581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 11345 16.80 - 33.61: 1509 33.61 - 50.41: 474 50.41 - 67.22: 157 67.22 - 84.02: 36 Dihedral angle restraints: 13521 sinusoidal: 5349 harmonic: 8172 Sorted by residual: dihedral pdb=" CD ARGDb 11 " pdb=" NE ARGDb 11 " pdb=" CZ ARGDb 11 " pdb=" NH1 ARGDb 11 " ideal model delta sinusoidal sigma weight residual 0.00 -83.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CD ARGDa 11 " pdb=" NE ARGDa 11 " pdb=" CZ ARGDa 11 " pdb=" NH1 ARGDa 11 " ideal model delta sinusoidal sigma weight residual 0.00 -83.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CD ARGDc 11 " pdb=" NE ARGDc 11 " pdb=" CZ ARGDc 11 " pdb=" NH1 ARGDc 11 " ideal model delta sinusoidal sigma weight residual 0.00 -83.41 83.41 1 1.00e+01 1.00e-02 8.50e+01 ... (remaining 13518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3083 0.093 - 0.186: 311 0.186 - 0.279: 44 0.279 - 0.372: 9 0.372 - 0.465: 3 Chirality restraints: 3450 Sorted by residual: chirality pdb=" CB VAL B 258 " pdb=" CA VAL B 258 " pdb=" CG1 VAL B 258 " pdb=" CG2 VAL B 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CB VAL F 258 " pdb=" CA VAL F 258 " pdb=" CG1 VAL F 258 " pdb=" CG2 VAL F 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CB VAL I 258 " pdb=" CA VAL I 258 " pdb=" CG1 VAL I 258 " pdb=" CG2 VAL I 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3447 not shown) Planarity restraints: 4050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGDc 11 " -1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARGDc 11 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARGDc 11 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARGDc 11 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARGDc 11 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDb 11 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARGDb 11 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARGDb 11 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARGDb 11 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARGDb 11 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDa 11 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARGDa 11 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARGDa 11 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARGDa 11 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARGDa 11 " 0.018 2.00e-02 2.50e+03 ... (remaining 4047 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 336 2.54 - 3.13: 17770 3.13 - 3.72: 40323 3.72 - 4.31: 60871 4.31 - 4.90: 98635 Nonbonded interactions: 217935 Sorted by model distance: nonbonded pdb=" NE2 HIS H 144 " pdb="CU CU H 501 " model vdw 1.944 3.060 nonbonded pdb=" NE2 HIS A 144 " pdb="CU CU A 501 " model vdw 1.944 3.060 nonbonded pdb=" NE2 HIS E 144 " pdb="CU CU E 501 " model vdw 1.944 3.060 nonbonded pdb=" ND1 HIS E 142 " pdb="CU CU E 501 " model vdw 2.066 3.060 nonbonded pdb=" ND1 HIS A 142 " pdb="CU CU A 501 " model vdw 2.066 3.060 ... (remaining 217930 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'F' } ncs_group { reference = chain 'Da' selection = chain 'Db' selection = chain 'Dc' } 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: 2.370 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 0.006 0.099 23898 Z= 0.467 Angle : 0.922 9.731 32586 Z= 0.628 Chirality : 0.061 0.465 3450 Planarity : 0.031 0.493 4050 Dihedral : 17.946 84.021 8313 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.77 % Favored : 94.02 % Rotamer: Outliers : 4.77 % Allowed : 23.47 % Favored : 71.77 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -0.75 (0.16), residues: 2826 helix: 0.10 (0.14), residues: 1383 sheet: 0.11 (0.26), residues: 408 loop : -1.47 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 260 TYR 0.015 0.001 TYR C 164 PHE 0.012 0.001 PHE J 50 TRP 0.026 0.001 TRP F 115 HIS 0.012 0.001 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.47 (23898) covalent geometry : angle 0.92180 / 0.63 (32586) hydrogen bonds : bond 0.17610 / 11.68 ( 1313) hydrogen bonds : angle 8.24065 / 5.86 ( 3777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 468 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 73 THR cc_start: 0.6605 (m) cc_final: 0.6286 (p) REVERT: B 253 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5068 (ptmt) REVERT: Da 8 THR cc_start: 0.4981 (OUTLIER) cc_final: 0.4564 (p) REVERT: Da 11 ARG cc_start: 0.4004 (OUTLIER) cc_final: 0.3715 (mtp180) REVERT: Db 23 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5721 (mt) REVERT: Dc 8 THR cc_start: 0.4486 (OUTLIER) cc_final: 0.4069 (m) REVERT: Dc 11 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.3858 (mtp-110) REVERT: F 256 ARG cc_start: 0.4770 (OUTLIER) cc_final: 0.4226 (ptt-90) REVERT: E 126 ASP cc_start: 0.6382 (m-30) cc_final: 0.6052 (m-30) REVERT: E 311 ASN cc_start: 0.6306 (p0) cc_final: 0.5998 (p0) outliers start: 115 outliers final: 12 residues processed: 560 average time/residue: 0.5067 time to fit residues: 333.5176 Evaluate side-chains 345 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 326 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 151 PRO Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain Da residue 8 THR Chi-restraints excluded: chain Da residue 11 ARG Chi-restraints excluded: chain Da residue 32 VAL Chi-restraints excluded: chain Db residue 8 THR Chi-restraints excluded: chain Db residue 11 ARG Chi-restraints excluded: chain Db residue 23 ILE Chi-restraints excluded: chain Dc residue 8 THR Chi-restraints excluded: chain Dc residue 11 ARG Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain J residue 151 PRO Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain E residue 351 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 HIS C 267 ASN A 38 HIS A 142 HIS A 144 HIS B 21 HIS B 43 HIS B 122 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 204 HIS I 207 GLN F 43 HIS F 90 GLN F 122 ASN F 204 HIS J 140 HIS ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 ASN G 140 HIS ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 267 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 HIS ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 132 ASN E 148 ASN E 163 ASN E 173 ASN E 261 ASN E 284 ASN ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143811 restraints weight = 23899.482| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 0.91 r_work: 0.3484 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 23898 Z= 0.192 Angle : 0.740 14.489 32586 Z= 0.388 Chirality : 0.048 0.231 3450 Planarity : 0.007 0.091 4050 Dihedral : 5.454 47.011 3139 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.25 % Favored : 95.51 % Rotamer: Outliers : 5.64 % Allowed : 22.80 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -0.15 (0.16), residues: 2826 helix: 0.66 (0.14), residues: 1428 sheet: 0.21 (0.26), residues: 408 loop : -1.28 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 145 TYR 0.034 0.002 TYR J 164 PHE 0.024 0.002 PHE J 215 TRP 0.027 0.002 TRP F 65 HIS 0.008 0.002 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (23898) covalent geometry : angle 0.74017 / 0.39 (32586) hydrogen bonds : bond 0.04813 / 3.19 ( 1313) hydrogen bonds : angle 5.72656 / 4.09 ( 3777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 417 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.6176 (mmm) cc_final: 0.5938 (mmm) REVERT: A 91 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 117 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7034 (mm) REVERT: A 306 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6509 (ptp) REVERT: B 276 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5454 (mttt) REVERT: I 181 THR cc_start: 0.7028 (p) cc_final: 0.6788 (p) REVERT: J 101 ASN cc_start: 0.7481 (m110) cc_final: 0.7275 (m110) REVERT: J 115 MET cc_start: 0.7393 (mtp) cc_final: 0.7171 (mtm) REVERT: J 163 MET cc_start: 0.5397 (ttp) cc_final: 0.5153 (ttp) REVERT: J 176 MET cc_start: 0.4738 (mtm) cc_final: 0.4192 (tmt) REVERT: G 19 ASP cc_start: 0.5992 (t0) cc_final: 0.5689 (t0) REVERT: G 20 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4928 (tpp) REVERT: E 57 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7346 (mm) REVERT: E 88 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6614 (mt0) REVERT: E 148 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7646 (m110) REVERT: E 320 GLU cc_start: 0.8001 (tt0) cc_final: 0.7792 (tt0) outliers start: 136 outliers final: 28 residues processed: 517 average time/residue: 0.5026 time to fit residues: 307.3007 Evaluate side-chains 375 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain J residue 209 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 413 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 389 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 150 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 258 ASN A 122 GLN A 362 GLN A 403 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 HIS ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 ASN ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS H 132 ASN H 144 HIS H 189 ASN H 263 HIS H 284 ASN H 362 GLN E 38 HIS E 132 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140860 restraints weight = 23655.813| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.95 r_work: 0.3434 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 23898 Z= 0.184 Angle : 0.684 21.730 32586 Z= 0.353 Chirality : 0.046 0.212 3450 Planarity : 0.006 0.087 4050 Dihedral : 4.721 39.089 3100 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.29 % Favored : 96.50 % Rotamer: Outliers : 4.60 % Allowed : 23.96 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.34 (0.16), residues: 2826 helix: 1.14 (0.14), residues: 1422 sheet: 0.32 (0.25), residues: 417 loop : -1.13 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 211 TYR 0.024 0.002 TYR C 164 PHE 0.016 0.002 PHE G 161 TRP 0.018 0.001 TRP G 209 HIS 0.010 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (23898) covalent geometry : angle 0.68371 / 0.35 (32586) hydrogen bonds : bond 0.04920 / 3.24 ( 1313) hydrogen bonds : angle 5.44757 / 3.89 ( 3777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 375 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 101 ASN cc_start: 0.7753 (t0) cc_final: 0.7427 (m-40) REVERT: C 178 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.5629 (ttm170) REVERT: C 209 TRP cc_start: 0.8211 (t60) cc_final: 0.7973 (t60) REVERT: C 249 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.5440 (t80) REVERT: A 73 THR cc_start: 0.8282 (m) cc_final: 0.7891 (p) REVERT: B 145 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.7063 (t160) REVERT: B 206 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: B 211 ARG cc_start: 0.6820 (ptp-110) cc_final: 0.6372 (mtt90) REVERT: I 64 TRP cc_start: 0.8202 (m100) cc_final: 0.7996 (m100) REVERT: F 5 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5712 (ttp-170) REVERT: F 11 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6320 (tmmt) REVERT: J 176 MET cc_start: 0.5440 (mtm) cc_final: 0.5138 (pp-130) REVERT: G 20 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5451 (tpp) REVERT: H 326 ILE cc_start: 0.7372 (mm) cc_final: 0.7079 (pt) REVERT: H 403 ASN cc_start: 0.8269 (m-40) cc_final: 0.7965 (m110) REVERT: E 123 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8585 (mt) REVERT: E 130 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: E 365 GLU cc_start: 0.7479 (tt0) cc_final: 0.7271 (mm-30) REVERT: E 396 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8460 (mtt) outliers start: 111 outliers final: 28 residues processed: 457 average time/residue: 0.5431 time to fit residues: 288.3008 Evaluate side-chains 354 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain Da residue 23 ILE Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain J residue 209 TRP Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 396 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 1.9990 chunk 239 optimal weight: 0.0470 chunk 72 optimal weight: 0.5980 chunk 211 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 362 GLN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 122 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 351 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136390 restraints weight = 24280.054| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.03 r_work: 0.3435 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23898 Z= 0.134 Angle : 0.606 9.934 32586 Z= 0.315 Chirality : 0.044 0.216 3450 Planarity : 0.005 0.069 4050 Dihedral : 4.542 39.506 3100 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 3.98 % Allowed : 24.05 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.62 (0.16), residues: 2826 helix: 1.40 (0.14), residues: 1425 sheet: 0.46 (0.25), residues: 420 loop : -1.06 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 48 TYR 0.028 0.001 TYR J 164 PHE 0.023 0.001 PHE G 161 TRP 0.037 0.001 TRP I 115 HIS 0.009 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23898) covalent geometry : angle 0.60578 / 0.32 (32586) hydrogen bonds : bond 0.04303 / 2.82 ( 1313) hydrogen bonds : angle 5.22452 / 3.71 ( 3777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 348 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: C 101 ASN cc_start: 0.7618 (t0) cc_final: 0.7292 (m110) REVERT: C 178 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6812 (mpt180) REVERT: C 249 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.5178 (t80) REVERT: A 73 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 130 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7469 (tp30) REVERT: A 143 MET cc_start: 0.8467 (mmm) cc_final: 0.8225 (mmm) REVERT: B 54 ASP cc_start: 0.8089 (t70) cc_final: 0.7856 (t70) REVERT: B 156 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: B 206 GLU cc_start: 0.8583 (tt0) cc_final: 0.8365 (tt0) REVERT: B 211 ARG cc_start: 0.6780 (ptp-110) cc_final: 0.6380 (mtt90) REVERT: B 276 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5438 (mttm) REVERT: I 44 MET cc_start: 0.8702 (ttp) cc_final: 0.8475 (ttm) REVERT: F 5 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.5947 (ttp-170) REVERT: F 11 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6379 (tmmt) REVERT: J 156 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7729 (ppp) REVERT: G 20 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5875 (tpp) REVERT: G 75 MET cc_start: 0.8676 (mmt) cc_final: 0.8143 (mmp) REVERT: H 143 MET cc_start: 0.8909 (mmm) cc_final: 0.8708 (mmm) REVERT: H 201 MET cc_start: 0.7910 (tpt) cc_final: 0.7674 (tpp) REVERT: H 270 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8395 (mm110) REVERT: H 403 ASN cc_start: 0.8361 (m-40) cc_final: 0.8045 (m110) REVERT: E 230 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: E 326 ILE cc_start: 0.7899 (mm) cc_final: 0.7635 (mm) REVERT: E 365 GLU cc_start: 0.7565 (tt0) cc_final: 0.7287 (mm-30) outliers start: 96 outliers final: 26 residues processed: 415 average time/residue: 0.5683 time to fit residues: 271.5821 Evaluate side-chains 340 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain Da residue 23 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 209 TRP Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 214 TRP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 389 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN A 132 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 173 ASN A 362 GLN I 207 GLN I 261 ASN F 63 GLN F 261 ASN H 163 ASN E 69 ASN E 144 HIS E 351 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121585 restraints weight = 23927.453| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.12 r_work: 0.3195 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.9544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23898 Z= 0.205 Angle : 0.750 13.113 32586 Z= 0.391 Chirality : 0.050 0.238 3450 Planarity : 0.006 0.075 4050 Dihedral : 5.200 44.142 3098 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.12 % Rotamer: Outliers : 4.48 % Allowed : 23.76 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.21 (0.16), residues: 2826 helix: 0.96 (0.14), residues: 1422 sheet: 0.44 (0.25), residues: 405 loop : -1.13 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 260 TYR 0.034 0.003 TYR C 164 PHE 0.023 0.002 PHE C 63 TRP 0.020 0.002 TRP F 65 HIS 0.009 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (23898) covalent geometry : angle 0.74965 / 0.39 (32586) hydrogen bonds : bond 0.06115 / 3.99 ( 1313) hydrogen bonds : angle 5.72320 / 4.10 ( 3777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 357 time to evaluate : 0.819 Fit side-chains REVERT: C 81 PHE cc_start: 0.7533 (t80) cc_final: 0.7287 (t80) REVERT: C 178 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (mpt180) REVERT: A 69 ASN cc_start: 0.8885 (m-40) cc_final: 0.8512 (m110) REVERT: A 143 MET cc_start: 0.8820 (mmm) cc_final: 0.8607 (mmm) REVERT: B 7 GLU cc_start: 0.7641 (tp30) cc_final: 0.7305 (tm-30) REVERT: B 64 TRP cc_start: 0.8216 (m100) cc_final: 0.7496 (m100) REVERT: B 211 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7171 (mtp180) REVERT: B 276 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5797 (mttm) REVERT: I 5 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7517 (ttm-80) REVERT: I 7 GLU cc_start: 0.7850 (tp30) cc_final: 0.6891 (pm20) REVERT: I 11 LYS cc_start: 0.7589 (tttt) cc_final: 0.7017 (tmmt) REVERT: I 276 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5561 (mmtt) REVERT: F 5 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6089 (ttp-170) REVERT: F 11 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7180 (tmmt) REVERT: J 18 TYR cc_start: 0.5498 (OUTLIER) cc_final: 0.4635 (p90) REVERT: J 62 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7327 (pm20) REVERT: J 78 MET cc_start: 0.8403 (mmm) cc_final: 0.8063 (mpm) REVERT: J 107 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: J 176 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8395 (ptm) REVERT: G 62 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7528 (pm20) REVERT: G 101 ASN cc_start: 0.8583 (m110) cc_final: 0.8233 (m-40) REVERT: G 176 MET cc_start: 0.8349 (ttp) cc_final: 0.8141 (ttp) REVERT: G 215 PHE cc_start: 0.3960 (OUTLIER) cc_final: 0.3432 (m-80) REVERT: G 216 MET cc_start: 0.4835 (tmm) cc_final: 0.4566 (tmt) REVERT: H 216 MET cc_start: 0.8660 (ptt) cc_final: 0.8412 (ptm) REVERT: H 403 ASN cc_start: 0.8537 (m-40) cc_final: 0.8255 (m-40) REVERT: E 49 MET cc_start: 0.8611 (mtm) cc_final: 0.8378 (mtm) REVERT: E 57 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8372 (mm) REVERT: E 230 ASP cc_start: 0.8119 (m-30) cc_final: 0.7687 (m-30) REVERT: E 381 MET cc_start: 0.5581 (mmm) cc_final: 0.4156 (ptm) outliers start: 108 outliers final: 38 residues processed: 433 average time/residue: 0.5622 time to fit residues: 279.9833 Evaluate side-chains 366 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 214 TRP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 115 optimal weight: 0.5980 chunk 235 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN A 43 GLN A 122 GLN A 144 HIS B 45 HIS I 43 HIS G 135 GLN H 144 HIS E 132 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 351 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.146964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125964 restraints weight = 23813.450| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.04 r_work: 0.3249 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.9586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23898 Z= 0.128 Angle : 0.608 10.437 32586 Z= 0.316 Chirality : 0.045 0.218 3450 Planarity : 0.006 0.070 4050 Dihedral : 4.764 45.588 3098 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.99 % Allowed : 24.75 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.54 (0.16), residues: 2826 helix: 1.35 (0.14), residues: 1422 sheet: 0.41 (0.25), residues: 405 loop : -1.08 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.021 0.001 TYR J 164 PHE 0.019 0.001 PHE C 63 TRP 0.028 0.001 TRP I 115 HIS 0.009 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (23898) covalent geometry : angle 0.60795 / 0.32 (32586) hydrogen bonds : bond 0.04679 / 3.06 ( 1313) hydrogen bonds : angle 5.28194 / 3.76 ( 3777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 340 time to evaluate : 0.696 Fit side-chains REVERT: C 178 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7466 (mpt180) REVERT: C 209 TRP cc_start: 0.8366 (t60) cc_final: 0.8138 (t60) REVERT: A 69 ASN cc_start: 0.8885 (m-40) cc_final: 0.8597 (m110) REVERT: A 143 MET cc_start: 0.8756 (mmm) cc_final: 0.8503 (mmm) REVERT: A 230 ASP cc_start: 0.8093 (t0) cc_final: 0.7757 (m-30) REVERT: A 251 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 362 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 7 GLU cc_start: 0.7824 (tp30) cc_final: 0.7482 (tm-30) REVERT: B 15 MET cc_start: 0.8512 (mtp) cc_final: 0.8300 (mtt) REVERT: B 64 TRP cc_start: 0.8274 (m100) cc_final: 0.7716 (m100) REVERT: B 276 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5861 (mttm) REVERT: I 11 LYS cc_start: 0.7599 (tttt) cc_final: 0.7052 (tmmt) REVERT: F 7 GLU cc_start: 0.7186 (pm20) cc_final: 0.6658 (tm-30) REVERT: F 11 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7193 (tmmt) REVERT: J 18 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.4467 (p90) REVERT: J 20 MET cc_start: 0.7463 (tmm) cc_final: 0.7161 (ttp) REVERT: J 62 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7433 (pm20) REVERT: J 78 MET cc_start: 0.8339 (mmm) cc_final: 0.8116 (mpp) REVERT: J 83 LEU cc_start: 0.8325 (tt) cc_final: 0.7743 (tp) REVERT: J 156 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7628 (ppp) REVERT: J 176 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8225 (ttp) REVERT: G 62 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7562 (pm20) REVERT: G 83 LEU cc_start: 0.8267 (tt) cc_final: 0.7750 (tp) REVERT: G 94 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.5919 (t0) REVERT: G 101 ASN cc_start: 0.8594 (m110) cc_final: 0.8262 (m-40) REVERT: G 215 PHE cc_start: 0.4107 (OUTLIER) cc_final: 0.3368 (m-80) REVERT: G 216 MET cc_start: 0.4995 (tmm) cc_final: 0.4766 (tmt) REVERT: H 381 MET cc_start: 0.5852 (mmt) cc_final: 0.5586 (mmm) REVERT: H 403 ASN cc_start: 0.8562 (m-40) cc_final: 0.8314 (m-40) REVERT: E 49 MET cc_start: 0.8584 (mtm) cc_final: 0.8318 (mtm) REVERT: E 230 ASP cc_start: 0.8310 (m-30) cc_final: 0.7948 (m-30) REVERT: E 365 GLU cc_start: 0.8240 (tt0) cc_final: 0.7950 (tp30) REVERT: E 381 MET cc_start: 0.5113 (mmm) cc_final: 0.3828 (ptm) outliers start: 72 outliers final: 25 residues processed: 390 average time/residue: 0.5632 time to fit residues: 253.5508 Evaluate side-chains 346 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 214 TRP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 226 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN A 122 GLN I 21 HIS G 135 GLN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134725 restraints weight = 24061.245| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.17 r_work: 0.3218 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.9652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23898 Z= 0.130 Angle : 0.604 9.651 32586 Z= 0.314 Chirality : 0.045 0.219 3450 Planarity : 0.006 0.071 4050 Dihedral : 4.682 45.310 3098 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 2.57 % Allowed : 24.67 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.64 (0.16), residues: 2826 helix: 1.41 (0.14), residues: 1422 sheet: 0.43 (0.25), residues: 405 loop : -0.99 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 93 TYR 0.024 0.001 TYR J 164 PHE 0.017 0.001 PHE C 63 TRP 0.028 0.001 TRP I 115 HIS 0.008 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (23898) covalent geometry : angle 0.60409 / 0.31 (32586) hydrogen bonds : bond 0.04660 / 3.04 ( 1313) hydrogen bonds : angle 5.23329 / 3.72 ( 3777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 0.762 Fit side-chains REVERT: C 141 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: A 69 ASN cc_start: 0.8868 (m-40) cc_final: 0.8596 (m110) REVERT: A 73 THR cc_start: 0.8999 (m) cc_final: 0.8611 (p) REVERT: A 143 MET cc_start: 0.8733 (mmm) cc_final: 0.8525 (mmm) REVERT: A 230 ASP cc_start: 0.8064 (t0) cc_final: 0.7762 (m-30) REVERT: A 362 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: B 7 GLU cc_start: 0.7837 (tp30) cc_final: 0.7473 (tm-30) REVERT: B 15 MET cc_start: 0.8528 (mtp) cc_final: 0.8267 (mtt) REVERT: B 64 TRP cc_start: 0.8257 (m100) cc_final: 0.7611 (m100) REVERT: B 276 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5965 (mttm) REVERT: I 11 LYS cc_start: 0.7570 (tttt) cc_final: 0.7022 (tmmt) REVERT: I 257 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7217 (pt) REVERT: F 5 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6517 (mtp85) REVERT: F 7 GLU cc_start: 0.7165 (pm20) cc_final: 0.6655 (tm-30) REVERT: F 11 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7144 (tmmt) REVERT: J 18 TYR cc_start: 0.4946 (OUTLIER) cc_final: 0.4065 (p90) REVERT: J 20 MET cc_start: 0.7643 (tmm) cc_final: 0.7266 (ttp) REVERT: J 62 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7335 (pm20) REVERT: J 83 LEU cc_start: 0.8289 (tt) cc_final: 0.7703 (tp) REVERT: J 156 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7609 (ppp) REVERT: J 176 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: G 62 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7453 (pm20) REVERT: G 83 LEU cc_start: 0.8242 (tt) cc_final: 0.7725 (tp) REVERT: G 94 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6037 (t0) REVERT: G 101 ASN cc_start: 0.8547 (m110) cc_final: 0.8181 (m-40) REVERT: G 176 MET cc_start: 0.8338 (ttp) cc_final: 0.8005 (ttp) REVERT: G 215 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3497 (m-80) REVERT: H 381 MET cc_start: 0.5895 (mmt) cc_final: 0.5665 (mmm) REVERT: H 403 ASN cc_start: 0.8516 (m-40) cc_final: 0.8252 (m-40) REVERT: E 49 MET cc_start: 0.8580 (mtm) cc_final: 0.8333 (mtm) REVERT: E 230 ASP cc_start: 0.8263 (m-30) cc_final: 0.7890 (m-30) REVERT: E 365 GLU cc_start: 0.8226 (tt0) cc_final: 0.7952 (tp30) outliers start: 62 outliers final: 27 residues processed: 360 average time/residue: 0.5683 time to fit residues: 236.2246 Evaluate side-chains 344 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 214 TRP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN J 244 GLN G 135 GLN E 69 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133225 restraints weight = 23874.217| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.16 r_work: 0.3198 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.9792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23898 Z= 0.141 Angle : 0.616 9.848 32586 Z= 0.321 Chirality : 0.045 0.221 3450 Planarity : 0.006 0.072 4050 Dihedral : 4.696 40.991 3098 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.75 % Favored : 95.97 % Rotamer: Outliers : 2.57 % Allowed : 24.63 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.66 (0.16), residues: 2826 helix: 1.42 (0.14), residues: 1425 sheet: 0.35 (0.25), residues: 423 loop : -0.94 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 260 TYR 0.025 0.002 TYR C 164 PHE 0.017 0.001 PHE C 63 TRP 0.030 0.001 TRP I 115 HIS 0.010 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (23898) covalent geometry : angle 0.61626 / 0.32 (32586) hydrogen bonds : bond 0.04833 / 3.15 ( 1313) hydrogen bonds : angle 5.24493 / 3.74 ( 3777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 315 time to evaluate : 0.946 Fit side-chains REVERT: C 101 ASN cc_start: 0.8075 (m-40) cc_final: 0.7420 (m110) REVERT: A 69 ASN cc_start: 0.8830 (m-40) cc_final: 0.8579 (m110) REVERT: A 73 THR cc_start: 0.9009 (m) cc_final: 0.8642 (p) REVERT: A 143 MET cc_start: 0.8739 (mmm) cc_final: 0.8523 (mmm) REVERT: A 230 ASP cc_start: 0.8108 (t0) cc_final: 0.7844 (m-30) REVERT: B 7 GLU cc_start: 0.7916 (tp30) cc_final: 0.7514 (tm-30) REVERT: B 64 TRP cc_start: 0.8282 (m100) cc_final: 0.7619 (m100) REVERT: B 276 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6028 (mttm) REVERT: Da 42 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6392 (mp) REVERT: I 7 GLU cc_start: 0.7917 (tp30) cc_final: 0.7561 (tm-30) REVERT: I 11 LYS cc_start: 0.7678 (tttt) cc_final: 0.7146 (tmmt) REVERT: F 5 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6015 (mtp85) REVERT: F 7 GLU cc_start: 0.7282 (pm20) cc_final: 0.6737 (tm-30) REVERT: F 11 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7174 (tmmt) REVERT: J 18 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4356 (p90) REVERT: J 20 MET cc_start: 0.7773 (tmm) cc_final: 0.7393 (ttp) REVERT: J 62 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7384 (pm20) REVERT: J 83 LEU cc_start: 0.8303 (tt) cc_final: 0.7738 (tp) REVERT: J 156 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7569 (ppp) REVERT: J 176 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (ttp) REVERT: G 62 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7476 (pm20) REVERT: G 83 LEU cc_start: 0.8176 (tt) cc_final: 0.7674 (tp) REVERT: G 94 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6201 (t0) REVERT: G 101 ASN cc_start: 0.8577 (m110) cc_final: 0.8215 (m-40) REVERT: G 176 MET cc_start: 0.8385 (ttp) cc_final: 0.8121 (ttp) REVERT: G 215 PHE cc_start: 0.4033 (OUTLIER) cc_final: 0.3457 (m-80) REVERT: H 381 MET cc_start: 0.5924 (mmt) cc_final: 0.5672 (mmm) REVERT: H 403 ASN cc_start: 0.8527 (m-40) cc_final: 0.8259 (m-40) REVERT: E 49 MET cc_start: 0.8595 (mtm) cc_final: 0.8358 (mtm) REVERT: E 230 ASP cc_start: 0.8256 (m-30) cc_final: 0.7894 (m-30) REVERT: E 251 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8115 (tt) REVERT: E 365 GLU cc_start: 0.8309 (tt0) cc_final: 0.8022 (tp30) REVERT: E 381 MET cc_start: 0.5562 (mmt) cc_final: 0.4921 (mmm) outliers start: 62 outliers final: 32 residues processed: 362 average time/residue: 0.5570 time to fit residues: 233.3686 Evaluate side-chains 343 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain Da residue 42 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 214 TRP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 274 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN G 267 ASN H 311 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133962 restraints weight = 24246.588| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.17 r_work: 0.3208 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.9885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23898 Z= 0.132 Angle : 0.603 9.633 32586 Z= 0.314 Chirality : 0.045 0.218 3450 Planarity : 0.006 0.072 4050 Dihedral : 4.648 40.353 3098 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.86 % Rotamer: Outliers : 2.45 % Allowed : 24.75 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.76 (0.16), residues: 2826 helix: 1.51 (0.14), residues: 1425 sheet: 0.40 (0.25), residues: 423 loop : -0.92 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 334 TYR 0.024 0.001 TYR J 164 PHE 0.016 0.001 PHE C 63 TRP 0.035 0.001 TRP I 115 HIS 0.010 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23898) covalent geometry : angle 0.60298 / 0.31 (32586) hydrogen bonds : bond 0.04666 / 3.04 ( 1313) hydrogen bonds : angle 5.20933 / 3.71 ( 3777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: C 141 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: A 69 ASN cc_start: 0.8829 (m-40) cc_final: 0.8591 (m110) REVERT: A 73 THR cc_start: 0.9005 (m) cc_final: 0.8701 (p) REVERT: A 230 ASP cc_start: 0.8210 (t0) cc_final: 0.7931 (m-30) REVERT: B 7 GLU cc_start: 0.7934 (tp30) cc_final: 0.7520 (tm-30) REVERT: B 64 TRP cc_start: 0.8281 (m100) cc_final: 0.7614 (m100) REVERT: B 276 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6018 (mttm) REVERT: Da 42 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6432 (mp) REVERT: I 7 GLU cc_start: 0.7927 (tp30) cc_final: 0.7578 (tm-30) REVERT: I 11 LYS cc_start: 0.7707 (tttt) cc_final: 0.7177 (tmmt) REVERT: F 5 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6172 (mtp85) REVERT: F 7 GLU cc_start: 0.7359 (pm20) cc_final: 0.6848 (tm-30) REVERT: F 11 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7194 (tmmt) REVERT: J 18 TYR cc_start: 0.5102 (OUTLIER) cc_final: 0.4389 (p90) REVERT: J 20 MET cc_start: 0.7869 (tmm) cc_final: 0.7410 (ttp) REVERT: J 62 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7396 (pm20) REVERT: J 83 LEU cc_start: 0.8311 (tt) cc_final: 0.7743 (tp) REVERT: J 156 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7627 (ppp) REVERT: J 176 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (ttp) REVERT: G 62 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7506 (pm20) REVERT: G 83 LEU cc_start: 0.8197 (tt) cc_final: 0.7666 (tp) REVERT: G 101 ASN cc_start: 0.8584 (m110) cc_final: 0.8215 (m-40) REVERT: G 176 MET cc_start: 0.8389 (ttp) cc_final: 0.8145 (ttp) REVERT: G 215 PHE cc_start: 0.4247 (OUTLIER) cc_final: 0.3207 (m-80) REVERT: H 381 MET cc_start: 0.5937 (mmt) cc_final: 0.5700 (mmm) REVERT: H 403 ASN cc_start: 0.8499 (m-40) cc_final: 0.8227 (m-40) REVERT: E 49 MET cc_start: 0.8602 (mtm) cc_final: 0.8347 (mtm) REVERT: E 230 ASP cc_start: 0.8267 (m-30) cc_final: 0.7894 (m-30) REVERT: E 251 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8125 (tt) REVERT: E 381 MET cc_start: 0.5445 (mmt) cc_final: 0.4784 (mmm) outliers start: 59 outliers final: 33 residues processed: 361 average time/residue: 0.6088 time to fit residues: 253.8080 Evaluate side-chains 345 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain Da residue 42 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 73 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS J 244 GLN J 267 ASN G 135 GLN G 258 ASN G 267 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136290 restraints weight = 24318.635| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.17 r_work: 0.3273 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.9945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23898 Z= 0.118 Angle : 0.585 9.393 32586 Z= 0.304 Chirality : 0.044 0.213 3450 Planarity : 0.005 0.071 4050 Dihedral : 4.569 42.133 3098 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.40 % Favored : 96.32 % Rotamer: Outliers : 1.70 % Allowed : 25.62 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: 0.82 (0.16), residues: 2826 helix: 1.54 (0.14), residues: 1437 sheet: 0.46 (0.25), residues: 423 loop : -0.92 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 334 TYR 0.022 0.001 TYR J 164 PHE 0.017 0.001 PHE C 63 TRP 0.043 0.001 TRP I 115 HIS 0.010 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (23898) covalent geometry : angle 0.58512 / 0.30 (32586) hydrogen bonds : bond 0.04361 / 2.85 ( 1313) hydrogen bonds : angle 5.12126 / 3.64 ( 3777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: C 59 MET cc_start: 0.8059 (mmm) cc_final: 0.7507 (mmt) REVERT: C 141 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: A 58 LYS cc_start: 0.8506 (ttmm) cc_final: 0.7834 (mtmt) REVERT: A 69 ASN cc_start: 0.8794 (m-40) cc_final: 0.8543 (m110) REVERT: A 73 THR cc_start: 0.9002 (m) cc_final: 0.8619 (p) REVERT: A 230 ASP cc_start: 0.8185 (t0) cc_final: 0.7917 (m-30) REVERT: A 362 GLN cc_start: 0.7965 (pt0) cc_final: 0.7724 (pt0) REVERT: A 381 MET cc_start: 0.5551 (mmt) cc_final: 0.5023 (mmm) REVERT: B 7 GLU cc_start: 0.7998 (tp30) cc_final: 0.7579 (tm-30) REVERT: B 64 TRP cc_start: 0.8259 (m100) cc_final: 0.7651 (m100) REVERT: B 276 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.5957 (mttm) REVERT: Da 42 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6448 (mp) REVERT: I 7 GLU cc_start: 0.7949 (tp30) cc_final: 0.7614 (tm-30) REVERT: I 11 LYS cc_start: 0.7712 (tttt) cc_final: 0.7213 (tmmt) REVERT: F 5 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6289 (mtp85) REVERT: F 7 GLU cc_start: 0.7318 (pm20) cc_final: 0.6884 (tm-30) REVERT: F 11 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7241 (tmmt) REVERT: J 20 MET cc_start: 0.7811 (tmm) cc_final: 0.7363 (ttp) REVERT: J 62 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7366 (pm20) REVERT: J 83 LEU cc_start: 0.8328 (tt) cc_final: 0.7624 (mp) REVERT: J 156 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7574 (ppp) REVERT: J 176 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: G 20 MET cc_start: 0.6846 (tpp) cc_final: 0.6607 (tpp) REVERT: G 62 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7521 (pm20) REVERT: G 78 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: G 83 LEU cc_start: 0.8225 (tt) cc_final: 0.7674 (tp) REVERT: G 101 ASN cc_start: 0.8606 (m110) cc_final: 0.8235 (m-40) REVERT: H 381 MET cc_start: 0.5837 (mmt) cc_final: 0.5623 (mmm) REVERT: H 403 ASN cc_start: 0.8510 (m-40) cc_final: 0.8260 (m-40) REVERT: E 49 MET cc_start: 0.8607 (mtm) cc_final: 0.8371 (mtm) REVERT: E 230 ASP cc_start: 0.8303 (m-30) cc_final: 0.7945 (m-30) REVERT: E 251 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8172 (tt) REVERT: E 381 MET cc_start: 0.5234 (mmt) cc_final: 0.4641 (mmm) outliers start: 41 outliers final: 25 residues processed: 348 average time/residue: 0.6049 time to fit residues: 242.6799 Evaluate side-chains 338 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain Da residue 42 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 13 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 154 optimal weight: 0.3980 chunk 214 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 135 GLN B 21 HIS J 47 GLN G 135 GLN G 267 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132506 restraints weight = 23946.680| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.16 r_work: 0.3163 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23898 Z= 0.146 Angle : 0.629 10.200 32586 Z= 0.327 Chirality : 0.046 0.222 3450 Planarity : 0.006 0.073 4050 Dihedral : 4.715 42.521 3098 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.03 % Favored : 95.65 % Rotamer: Outliers : 1.95 % Allowed : 25.37 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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 (0.16), residues: 2826 helix: 1.48 (0.14), residues: 1437 sheet: 0.46 (0.25), residues: 423 loop : -0.92 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 334 TYR 0.026 0.002 TYR J 164 PHE 0.016 0.002 PHE G 81 TRP 0.049 0.001 TRP I 115 HIS 0.011 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23898) covalent geometry : angle 0.62912 / 0.33 (32586) hydrogen bonds : bond 0.04946 / 3.22 ( 1313) hydrogen bonds : angle 5.26399 / 3.74 ( 3777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7115.18 seconds wall clock time: 121 minutes 57.31 seconds (7317.31 seconds total)