Starting phenix.real_space_refine on Fri Jun 20 10:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_45663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_45663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_45663.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_45663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl6_45663/06_2025/9cl6_45663.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "Db" 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, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 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: E, H, G, J, Dc, Da, F, I Time building chain proxies: 17.35, per 1000 atoms: 0.73 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: 6.49 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.67 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: 9.05 Time building geometry restraints manager: 7.66 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 2.320 nonbonded pdb=" NE2 HIS A 144 " pdb="CU CU A 501 " model vdw 1.944 2.320 nonbonded pdb=" NE2 HIS E 144 " pdb="CU CU E 501 " model vdw 1.944 2.320 nonbonded pdb=" ND1 HIS E 142 " pdb="CU CU E 501 " model vdw 2.066 2.320 nonbonded pdb=" ND1 HIS A 142 " pdb="CU CU A 501 " model vdw 2.066 2.320 ... (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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'Db' selection = chain 'Dc' selection = chain 'Da' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' } 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: 2.450 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: 0.050 Extract box with map and model: 1.290 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 60.160 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.001 TRP F 115 HIS 0.012 0.001 HIS H 142 PHE 0.012 0.001 PHE J 50 TYR 0.015 0.001 TYR C 164 ARG 0.006 0.001 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.17610 ( 1313) hydrogen bonds : angle 8.24065 ( 3777) covalent geometry : bond 0.00647 (23898) covalent geometry : angle 0.92180 (32586) *********************** 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 : 2.461 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: 0.5066 (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: 0.3714 (mtp180) REVERT: Db 23 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5722 (mt) REVERT: Dc 8 THR cc_start: 0.4486 (OUTLIER) cc_final: 0.4075 (m) REVERT: Dc 11 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.3861 (mtp-110) REVERT: F 256 ARG cc_start: 0.4770 (OUTLIER) cc_final: 0.4224 (ptt-90) REVERT: E 126 ASP cc_start: 0.6382 (m-30) cc_final: 0.6055 (m-30) REVERT: E 311 ASN cc_start: 0.6306 (p0) cc_final: 0.5997 (p0) outliers start: 115 outliers final: 12 residues processed: 560 average time/residue: 1.3465 time to fit residues: 882.2537 Evaluate side-chains 342 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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 235 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 218 optimal weight: 0.0770 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 ASN 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 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 267 ASN H 38 HIS H 88 GLN H 405 HIS E 38 HIS E 53 GLN E 132 ASN E 163 ASN E 173 ASN E 261 ASN E 284 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.162777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144097 restraints weight = 24826.424| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 0.96 r_work: 0.3486 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23898 Z= 0.202 Angle : 0.742 14.837 32586 Z= 0.390 Chirality : 0.048 0.275 3450 Planarity : 0.007 0.087 4050 Dihedral : 5.456 42.931 3139 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.35 % Favored : 95.40 % Rotamer: Outliers : 5.76 % Allowed : 22.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2826 helix: 0.65 (0.14), residues: 1425 sheet: 0.17 (0.26), residues: 408 loop : -1.29 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 65 HIS 0.009 0.001 HIS F 204 PHE 0.032 0.002 PHE J 215 TYR 0.036 0.002 TYR J 164 ARG 0.012 0.001 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 1313) hydrogen bonds : angle 5.70494 ( 3777) covalent geometry : bond 0.00404 (23898) covalent geometry : angle 0.74177 (32586) *********************** 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 556 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 417 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 117 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7052 (mm) REVERT: A 306 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6437 (ptp) REVERT: A 388 GLU cc_start: 0.7222 (tt0) cc_final: 0.6882 (tt0) REVERT: B 276 LYS cc_start: 0.5703 (OUTLIER) cc_final: 0.5482 (mttt) REVERT: I 181 THR cc_start: 0.7014 (p) cc_final: 0.6773 (p) REVERT: I 256 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5829 (mtm180) REVERT: J 101 ASN cc_start: 0.7467 (m110) cc_final: 0.7262 (m110) REVERT: J 115 MET cc_start: 0.7359 (mtp) cc_final: 0.7154 (mtm) REVERT: J 163 MET cc_start: 0.5366 (ttp) cc_final: 0.5156 (ttp) REVERT: J 176 MET cc_start: 0.4716 (mtm) cc_final: 0.4214 (tmt) REVERT: G 19 ASP cc_start: 0.5982 (t0) cc_final: 0.5699 (t0) REVERT: G 20 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4209 (tmm) REVERT: E 57 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7328 (mm) REVERT: E 88 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6580 (mm110) REVERT: E 320 GLU cc_start: 0.8002 (tt0) cc_final: 0.7787 (tt0) outliers start: 139 outliers final: 32 residues processed: 519 average time/residue: 1.1906 time to fit residues: 726.2524 Evaluate side-chains 373 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 146 MET 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 256 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain Da residue 23 ILE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 256 ARG Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain F residue 45 HIS 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 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 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 85 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 258 ASN A 38 HIS A 77 HIS A 88 GLN A 122 GLN A 142 HIS 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 47 GLN G 135 GLN G 153 HIS ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS H 189 ASN H 263 HIS H 284 ASN H 362 GLN E 132 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140133 restraints weight = 24781.302| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.01 r_work: 0.3457 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23898 Z= 0.172 Angle : 0.686 13.745 32586 Z= 0.356 Chirality : 0.046 0.213 3450 Planarity : 0.006 0.076 4050 Dihedral : 4.763 38.033 3100 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.21 % Rotamer: Outliers : 4.73 % Allowed : 23.92 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2826 helix: 1.11 (0.14), residues: 1416 sheet: 0.50 (0.26), residues: 399 loop : -1.17 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 23 HIS 0.011 0.001 HIS I 45 PHE 0.022 0.002 PHE C 213 TYR 0.025 0.002 TYR J 164 ARG 0.029 0.001 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.05223 ( 1313) hydrogen bonds : angle 5.47229 ( 3777) covalent geometry : bond 0.00369 (23898) covalent geometry : angle 0.68646 (32586) *********************** 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 506 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 392 time to evaluate : 2.639 Fit side-chains revert: symmetry clash REVERT: C 101 ASN cc_start: 0.7740 (t0) cc_final: 0.7384 (m-40) REVERT: C 216 MET cc_start: 0.4903 (tmt) cc_final: 0.3305 (pp-130) REVERT: C 249 TYR cc_start: 0.7437 (m-80) cc_final: 0.6127 (t80) REVERT: A 73 THR cc_start: 0.8387 (m) cc_final: 0.7941 (p) REVERT: B 206 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: B 211 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6356 (mtt90) REVERT: B 251 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5305 (mttp) REVERT: I 44 MET cc_start: 0.8597 (ttp) cc_final: 0.8367 (ttm) REVERT: I 64 TRP cc_start: 0.8224 (m100) cc_final: 0.7977 (m100) REVERT: F 5 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.5556 (ttp-170) REVERT: F 11 LYS cc_start: 0.7139 (ttmt) cc_final: 0.6282 (tmmt) REVERT: F 185 MET cc_start: 0.8358 (tpt) cc_final: 0.8041 (tpt) REVERT: J 223 PRO cc_start: 0.8449 (Cg_endo) cc_final: 0.8245 (Cg_exo) REVERT: G 215 PHE cc_start: 0.3605 (OUTLIER) cc_final: 0.3381 (m-80) REVERT: H 381 MET cc_start: 0.5348 (mmt) cc_final: 0.4810 (mtp) REVERT: H 403 ASN cc_start: 0.8282 (m-40) cc_final: 0.7947 (m-40) REVERT: E 57 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7997 (mm) REVERT: E 123 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 130 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: E 396 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8590 (mtt) outliers start: 114 outliers final: 27 residues processed: 473 average time/residue: 1.4246 time to fit residues: 776.4414 Evaluate side-chains 347 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 132 ASN 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 B residue 145 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain Da residue 23 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 209 TRP Chi-restraints excluded: chain J residue 214 TRP Chi-restraints excluded: chain J residue 266 ASN 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 133 LEU Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain E residue 57 ILE 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 305 THR Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 316 VAL 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 93 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 276 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 273 GLN A 362 GLN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 261 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN H 43 GLN H 132 ASN E 351 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129836 restraints weight = 25364.373| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.13 r_work: 0.3328 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23898 Z= 0.157 Angle : 0.637 9.975 32586 Z= 0.331 Chirality : 0.046 0.217 3450 Planarity : 0.006 0.093 4050 Dihedral : 4.650 37.671 3100 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 3.86 % Allowed : 24.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2826 helix: 1.36 (0.14), residues: 1416 sheet: 0.44 (0.25), residues: 420 loop : -1.17 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP I 115 HIS 0.009 0.001 HIS I 45 PHE 0.014 0.002 PHE B 92 TYR 0.028 0.002 TYR J 164 ARG 0.009 0.001 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 1313) hydrogen bonds : angle 5.25616 ( 3777) covalent geometry : bond 0.00349 (23898) covalent geometry : angle 0.63652 (32586) *********************** 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 432 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 339 time to evaluate : 3.507 Fit side-chains REVERT: C 78 MET cc_start: 0.8038 (mmt) cc_final: 0.7812 (mpp) REVERT: C 101 ASN cc_start: 0.7793 (t0) cc_final: 0.7441 (m110) REVERT: C 209 TRP cc_start: 0.8086 (t60) cc_final: 0.7849 (t60) REVERT: C 215 PHE cc_start: 0.4090 (OUTLIER) cc_final: 0.3771 (t80) REVERT: C 216 MET cc_start: 0.4597 (tmt) cc_final: 0.2952 (pp-130) REVERT: A 130 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7549 (tp30) REVERT: A 132 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: A 311 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7387 (m110) REVERT: A 343 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7749 (mmt180) REVERT: B 7 GLU cc_start: 0.6986 (tp30) cc_final: 0.6347 (pm20) REVERT: B 64 TRP cc_start: 0.7910 (m100) cc_final: 0.6965 (m100) REVERT: B 211 ARG cc_start: 0.6695 (ptp-110) cc_final: 0.6431 (mtp-110) REVERT: I 44 MET cc_start: 0.8879 (ttp) cc_final: 0.8648 (ttm) REVERT: I 64 TRP cc_start: 0.8307 (m100) cc_final: 0.8060 (m100) REVERT: I 257 ILE cc_start: 0.6729 (pt) cc_final: 0.6509 (pp) REVERT: F 5 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.5639 (ttp-170) REVERT: F 11 LYS cc_start: 0.7561 (ttmt) cc_final: 0.6579 (tmmt) REVERT: J 107 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: J 156 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7668 (ppp) REVERT: G 75 MET cc_start: 0.8562 (mmt) cc_final: 0.8276 (mmp) REVERT: G 215 PHE cc_start: 0.3649 (OUTLIER) cc_final: 0.3240 (m-80) REVERT: H 201 MET cc_start: 0.8007 (tpt) cc_final: 0.7744 (tpp) REVERT: H 403 ASN cc_start: 0.8417 (m-40) cc_final: 0.7995 (m-40) REVERT: E 69 ASN cc_start: 0.8729 (m-40) cc_final: 0.8442 (m110) REVERT: E 230 ASP cc_start: 0.7920 (m-30) cc_final: 0.7396 (m-30) REVERT: E 320 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: E 396 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8557 (mtt) outliers start: 93 outliers final: 27 residues processed: 405 average time/residue: 1.4278 time to fit residues: 663.0701 Evaluate side-chains 338 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain A residue 132 ASN 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 362 GLN Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 202 VAL 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 I residue 275 ILE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 107 GLU 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 254 ASP Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 396 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 164 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN I 261 ASN F 63 GLN F 261 ASN J 47 GLN G 47 GLN G 135 GLN G 267 ASN H 69 ASN H 142 HIS H 163 ASN H 173 ASN E 351 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116113 restraints weight = 25678.289| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.21 r_work: 0.3257 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.9467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23898 Z= 0.202 Angle : 0.736 10.451 32586 Z= 0.385 Chirality : 0.049 0.240 3450 Planarity : 0.007 0.093 4050 Dihedral : 5.144 42.304 3099 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.53 % Favored : 95.26 % Rotamer: Outliers : 3.98 % Allowed : 23.63 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2826 helix: 1.04 (0.14), residues: 1416 sheet: 0.37 (0.25), residues: 405 loop : -1.15 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 115 HIS 0.010 0.001 HIS B 43 PHE 0.021 0.002 PHE B 213 TYR 0.036 0.002 TYR C 164 ARG 0.007 0.001 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.06104 ( 1313) hydrogen bonds : angle 5.61757 ( 3777) covalent geometry : bond 0.00472 (23898) covalent geometry : angle 0.73591 (32586) *********************** 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 438 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 342 time to evaluate : 2.644 Fit side-chains REVERT: C 78 MET cc_start: 0.8258 (mmt) cc_final: 0.7992 (mpp) REVERT: C 81 PHE cc_start: 0.7447 (t80) cc_final: 0.7211 (t80) REVERT: A 69 ASN cc_start: 0.8879 (m-40) cc_final: 0.8443 (m110) REVERT: A 130 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8047 (tt0) REVERT: A 143 MET cc_start: 0.8907 (mmm) cc_final: 0.8657 (mmm) REVERT: A 359 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8400 (mm-40) REVERT: A 381 MET cc_start: 0.6754 (mmt) cc_final: 0.6425 (mmm) REVERT: B 7 GLU cc_start: 0.7606 (tp30) cc_final: 0.7230 (tm-30) REVERT: B 64 TRP cc_start: 0.8213 (m100) cc_final: 0.7437 (m100) REVERT: B 211 ARG cc_start: 0.7092 (ptp-110) cc_final: 0.6872 (mtp-110) REVERT: I 11 LYS cc_start: 0.7414 (tttt) cc_final: 0.6870 (tmmt) REVERT: I 256 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6713 (mtm180) REVERT: F 11 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7112 (tmmt) REVERT: J 18 TYR cc_start: 0.5594 (OUTLIER) cc_final: 0.4693 (p90) REVERT: J 62 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7220 (pm20) REVERT: J 78 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7703 (tpp) REVERT: J 83 LEU cc_start: 0.8183 (tt) cc_final: 0.7554 (tp) REVERT: J 107 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: G 62 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7377 (pm20) REVERT: G 101 ASN cc_start: 0.8493 (m110) cc_final: 0.8035 (m-40) REVERT: G 156 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7935 (ptt) REVERT: G 215 PHE cc_start: 0.4082 (OUTLIER) cc_final: 0.3500 (m-80) REVERT: H 381 MET cc_start: 0.5755 (mmt) cc_final: 0.4738 (mtp) REVERT: H 403 ASN cc_start: 0.8520 (m-40) cc_final: 0.8193 (m-40) REVERT: E 49 MET cc_start: 0.8560 (mtm) cc_final: 0.8272 (mtm) REVERT: E 230 ASP cc_start: 0.8133 (m-30) cc_final: 0.7741 (m-30) REVERT: E 320 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: E 381 MET cc_start: 0.5774 (mmm) cc_final: 0.4270 (ptm) REVERT: E 396 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8819 (mtt) outliers start: 96 outliers final: 31 residues processed: 412 average time/residue: 1.4443 time to fit residues: 685.3552 Evaluate side-chains 347 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER 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 B residue 23 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 256 ARG Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 78 MET Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 122 ILE 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 156 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 316 VAL 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 316 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 396 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 172 optimal weight: 0.1980 chunk 264 optimal weight: 0.7980 chunk 143 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN A 43 GLN I 21 HIS ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN G 135 GLN G 267 ASN E 132 ASN E 163 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130293 restraints weight = 24202.101| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.90 r_work: 0.3311 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.9531 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= 0.121 Angle : 0.589 8.235 32586 Z= 0.307 Chirality : 0.044 0.214 3450 Planarity : 0.005 0.068 4050 Dihedral : 4.676 43.477 3099 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.74 % Allowed : 24.75 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2826 helix: 1.43 (0.14), residues: 1422 sheet: 0.38 (0.25), residues: 402 loop : -1.02 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP I 115 HIS 0.007 0.001 HIS F 45 PHE 0.012 0.001 PHE H 94 TYR 0.018 0.001 TYR J 164 ARG 0.007 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1313) hydrogen bonds : angle 5.18229 ( 3777) covalent geometry : bond 0.00256 (23898) covalent geometry : angle 0.58917 (32586) *********************** 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 391 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 2.356 Fit side-chains revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8818 (m-40) cc_final: 0.8527 (m110) REVERT: A 251 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 381 MET cc_start: 0.6089 (mmt) cc_final: 0.5774 (mmm) REVERT: B 7 GLU cc_start: 0.7733 (tp30) cc_final: 0.7415 (tm-30) REVERT: B 64 TRP cc_start: 0.8205 (m100) cc_final: 0.7590 (m100) REVERT: B 128 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6796 (pp) REVERT: I 11 LYS cc_start: 0.7322 (tttt) cc_final: 0.6828 (tmmt) REVERT: I 256 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6522 (mtm180) REVERT: F 5 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6405 (mtp85) REVERT: F 7 GLU cc_start: 0.7047 (pm20) cc_final: 0.6602 (tm-30) REVERT: F 11 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7188 (tmmt) REVERT: J 18 TYR cc_start: 0.5330 (OUTLIER) cc_final: 0.4492 (p90) REVERT: J 20 MET cc_start: 0.7535 (tmm) cc_final: 0.7151 (ttp) REVERT: J 62 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7435 (pm20) REVERT: J 83 LEU cc_start: 0.8282 (tt) cc_final: 0.7685 (tp) REVERT: J 156 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7654 (ppp) REVERT: J 176 MET cc_start: 0.8372 (ppp) cc_final: 0.8101 (ptm) REVERT: G 62 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7437 (pm20) REVERT: G 83 LEU cc_start: 0.8216 (tt) cc_final: 0.7684 (tp) REVERT: G 101 ASN cc_start: 0.8424 (m110) cc_final: 0.7983 (m-40) REVERT: G 215 PHE cc_start: 0.4107 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: G 216 MET cc_start: 0.5036 (tmm) cc_final: 0.4594 (tmt) REVERT: H 403 ASN cc_start: 0.8540 (m-40) cc_final: 0.8283 (m-40) REVERT: E 49 MET cc_start: 0.8562 (mtm) cc_final: 0.8286 (mtm) REVERT: E 230 ASP cc_start: 0.8237 (m-30) cc_final: 0.7868 (m-30) outliers start: 66 outliers final: 17 residues processed: 369 average time/residue: 1.4298 time to fit residues: 603.7050 Evaluate side-chains 327 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 416 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 256 ARG Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain J residue 266 ASN 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 H residue 104 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain E residue 104 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 23 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 311 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN G 135 GLN G 267 ASN E 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118202 restraints weight = 25263.185| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.03 r_work: 0.3134 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.9894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 23898 Z= 0.238 Angle : 0.731 10.706 32586 Z= 0.384 Chirality : 0.051 0.240 3450 Planarity : 0.007 0.078 4050 Dihedral : 5.183 44.547 3099 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.49 % Favored : 95.22 % Rotamer: Outliers : 2.86 % Allowed : 24.05 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2826 helix: 1.02 (0.14), residues: 1419 sheet: 0.40 (0.25), residues: 402 loop : -1.07 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 115 HIS 0.012 0.001 HIS B 43 PHE 0.019 0.002 PHE B 213 TYR 0.036 0.003 TYR G 164 ARG 0.009 0.001 ARG J 145 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 1313) hydrogen bonds : angle 5.61357 ( 3777) covalent geometry : bond 0.00583 (23898) covalent geometry : angle 0.73095 (32586) *********************** 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 384 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 2.628 Fit side-chains revert: symmetry clash REVERT: C 81 PHE cc_start: 0.7938 (t80) cc_final: 0.7651 (t80) REVERT: C 144 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7648 (mp) REVERT: C 216 MET cc_start: 0.3751 (tmt) cc_final: 0.2175 (ppp) REVERT: A 69 ASN cc_start: 0.8940 (m-40) cc_final: 0.8608 (m110) REVERT: A 230 ASP cc_start: 0.8353 (t0) cc_final: 0.8066 (m-30) REVERT: A 381 MET cc_start: 0.6610 (mmt) cc_final: 0.6349 (mmm) REVERT: B 7 GLU cc_start: 0.7960 (tp30) cc_final: 0.7615 (tm-30) REVERT: B 64 TRP cc_start: 0.8376 (m100) cc_final: 0.7711 (m100) REVERT: I 7 GLU cc_start: 0.8160 (tp30) cc_final: 0.7851 (tm-30) REVERT: I 11 LYS cc_start: 0.7838 (tttt) cc_final: 0.7347 (tmmt) REVERT: I 232 MET cc_start: 0.8549 (tpp) cc_final: 0.8331 (mmt) REVERT: F 5 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6152 (mtp85) REVERT: F 7 GLU cc_start: 0.7433 (pm20) cc_final: 0.6961 (tm-30) REVERT: F 11 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7464 (tmmt) REVERT: J 18 TYR cc_start: 0.5450 (OUTLIER) cc_final: 0.4541 (p90) REVERT: J 20 MET cc_start: 0.7928 (tmm) cc_final: 0.7441 (ttp) REVERT: J 62 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7505 (pm20) REVERT: J 83 LEU cc_start: 0.8352 (tt) cc_final: 0.7800 (tp) REVERT: J 156 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: G 62 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7686 (pm20) REVERT: G 83 LEU cc_start: 0.8341 (tt) cc_final: 0.7833 (tp) REVERT: G 94 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6550 (t0) REVERT: G 101 ASN cc_start: 0.8722 (m110) cc_final: 0.8285 (m-40) REVERT: G 144 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7704 (mt) REVERT: G 215 PHE cc_start: 0.4440 (OUTLIER) cc_final: 0.3234 (m-80) REVERT: G 216 MET cc_start: 0.5125 (tmm) cc_final: 0.4761 (tmt) REVERT: E 49 MET cc_start: 0.8679 (mtm) cc_final: 0.8428 (mtm) REVERT: E 230 ASP cc_start: 0.8319 (m-30) cc_final: 0.7906 (m-30) outliers start: 69 outliers final: 27 residues processed: 367 average time/residue: 1.4047 time to fit residues: 589.1626 Evaluate side-chains 333 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 144 ILE 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 416 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain J residue 18 TYR Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 156 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 144 ILE 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 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 365 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 110 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119396 restraints weight = 25092.385| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.04 r_work: 0.3160 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 1.0024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23898 Z= 0.185 Angle : 0.669 10.457 32586 Z= 0.351 Chirality : 0.048 0.230 3450 Planarity : 0.006 0.077 4050 Dihedral : 5.025 45.266 3099 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.96 % Favored : 95.79 % Rotamer: Outliers : 2.32 % Allowed : 24.46 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2826 helix: 1.15 (0.14), residues: 1410 sheet: 0.40 (0.25), residues: 402 loop : -1.03 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 115 HIS 0.009 0.001 HIS I 45 PHE 0.017 0.002 PHE E 94 TYR 0.030 0.002 TYR C 164 ARG 0.005 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 1313) hydrogen bonds : angle 5.48315 ( 3777) covalent geometry : bond 0.00444 (23898) covalent geometry : angle 0.66917 (32586) *********************** 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 362 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 2.761 Fit side-chains revert: symmetry clash REVERT: C 216 MET cc_start: 0.3385 (tmt) cc_final: 0.2039 (ppp) REVERT: A 69 ASN cc_start: 0.8943 (m-40) cc_final: 0.8661 (m110) REVERT: A 230 ASP cc_start: 0.8368 (t0) cc_final: 0.8124 (m-30) REVERT: A 251 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 7 GLU cc_start: 0.7962 (tp30) cc_final: 0.7646 (tm-30) REVERT: B 64 TRP cc_start: 0.8377 (m100) cc_final: 0.7748 (m100) REVERT: B 128 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7293 (pp) REVERT: I 7 GLU cc_start: 0.8150 (tp30) cc_final: 0.7846 (tm-30) REVERT: I 11 LYS cc_start: 0.7861 (tttt) cc_final: 0.7285 (tmmt) REVERT: F 5 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6386 (mtp85) REVERT: F 7 GLU cc_start: 0.7494 (pm20) cc_final: 0.7072 (tm-30) REVERT: F 11 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7451 (tmmt) REVERT: J 18 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4770 (p90) REVERT: J 20 MET cc_start: 0.8011 (tmm) cc_final: 0.7755 (ttp) REVERT: J 62 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7493 (pm20) REVERT: J 83 LEU cc_start: 0.8352 (tt) cc_final: 0.7694 (mp) REVERT: J 156 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7905 (ppp) REVERT: J 267 ASN cc_start: 0.7886 (t0) cc_final: 0.7646 (t160) REVERT: G 62 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7676 (pm20) REVERT: G 83 LEU cc_start: 0.8304 (tt) cc_final: 0.7789 (tp) REVERT: G 94 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6741 (t0) REVERT: G 101 ASN cc_start: 0.8657 (m110) cc_final: 0.8205 (m-40) REVERT: G 144 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7701 (mt) REVERT: G 215 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3232 (m-80) REVERT: G 216 MET cc_start: 0.5105 (tmm) cc_final: 0.4729 (tmt) REVERT: E 49 MET cc_start: 0.8686 (mtm) cc_final: 0.8478 (mtm) REVERT: E 230 ASP cc_start: 0.8309 (m-30) cc_final: 0.7907 (m-30) REVERT: E 251 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8186 (tt) REVERT: E 351 ASN cc_start: 0.8050 (p0) cc_final: 0.7827 (p0) outliers start: 56 outliers final: 27 residues processed: 346 average time/residue: 1.4294 time to fit residues: 565.0135 Evaluate side-chains 328 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain A residue 104 VAL 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 314 ILE 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 128 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain F residue 5 ARG 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 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 144 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 6 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN A 403 ASN ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.143461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123816 restraints weight = 24976.965| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.02 r_work: 0.3228 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 1.0072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23898 Z= 0.127 Angle : 0.600 9.654 32586 Z= 0.314 Chirality : 0.044 0.218 3450 Planarity : 0.006 0.072 4050 Dihedral : 4.758 44.639 3099 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.89 % Favored : 95.82 % Rotamer: Outliers : 2.03 % Allowed : 24.79 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2826 helix: 1.34 (0.14), residues: 1431 sheet: 0.47 (0.26), residues: 402 loop : -0.97 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 115 HIS 0.009 0.001 HIS I 45 PHE 0.014 0.001 PHE E 94 TYR 0.023 0.001 TYR C 164 ARG 0.006 0.000 ARG H 334 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 1313) hydrogen bonds : angle 5.26096 ( 3777) covalent geometry : bond 0.00278 (23898) covalent geometry : angle 0.59992 (32586) *********************** 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 359 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: C 20 MET cc_start: 0.6920 (ttm) cc_final: 0.6634 (tpp) REVERT: C 216 MET cc_start: 0.2962 (tmt) cc_final: 0.1775 (ppp) REVERT: A 69 ASN cc_start: 0.8914 (m-40) cc_final: 0.8686 (m110) REVERT: A 230 ASP cc_start: 0.8320 (t0) cc_final: 0.8106 (m-30) REVERT: A 251 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8344 (tt) REVERT: B 7 GLU cc_start: 0.7929 (tp30) cc_final: 0.7580 (tm-30) REVERT: B 64 TRP cc_start: 0.8332 (m100) cc_final: 0.7733 (m100) REVERT: B 128 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6874 (pp) REVERT: B 211 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7227 (mtt-85) REVERT: I 7 GLU cc_start: 0.8050 (tp30) cc_final: 0.7728 (tm-30) REVERT: I 11 LYS cc_start: 0.7776 (tttt) cc_final: 0.7219 (tmmt) REVERT: F 5 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6415 (mtp85) REVERT: F 7 GLU cc_start: 0.7377 (pm20) cc_final: 0.6885 (tm-30) REVERT: F 8 GLU cc_start: 0.7555 (tt0) cc_final: 0.7263 (tt0) REVERT: F 11 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7396 (tmmt) REVERT: J 20 MET cc_start: 0.8000 (tmm) cc_final: 0.7773 (ttp) REVERT: J 62 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7465 (pm20) REVERT: J 83 LEU cc_start: 0.8329 (tt) cc_final: 0.7654 (mp) REVERT: J 156 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7730 (ppp) REVERT: G 20 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7051 (ttp) REVERT: G 62 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7609 (pm20) REVERT: G 83 LEU cc_start: 0.8276 (tt) cc_final: 0.7746 (tp) REVERT: G 101 ASN cc_start: 0.8613 (m110) cc_final: 0.8129 (m-40) REVERT: G 215 PHE cc_start: 0.4493 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: G 216 MET cc_start: 0.4939 (tmm) cc_final: 0.4571 (tmt) REVERT: E 230 ASP cc_start: 0.8272 (m-30) cc_final: 0.7940 (m-30) REVERT: E 251 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8185 (tt) REVERT: E 351 ASN cc_start: 0.7964 (p0) cc_final: 0.7749 (p0) REVERT: E 381 MET cc_start: 0.5558 (mmp) cc_final: 0.5309 (mmm) outliers start: 49 outliers final: 26 residues processed: 343 average time/residue: 1.5009 time to fit residues: 593.4918 Evaluate side-chains 333 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER 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 416 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 211 ARG 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 J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 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 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 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 93 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 235 optimal weight: 0.0010 chunk 139 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN A 273 GLN A 403 ASN B 21 HIS ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 ASN E 273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123315 restraints weight = 25009.072| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.07 r_work: 0.3198 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 1.0125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23898 Z= 0.137 Angle : 0.614 9.698 32586 Z= 0.320 Chirality : 0.045 0.221 3450 Planarity : 0.006 0.073 4050 Dihedral : 4.739 44.277 3099 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.64 % Favored : 96.04 % Rotamer: Outliers : 1.66 % Allowed : 25.33 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2826 helix: 1.49 (0.14), residues: 1416 sheet: 0.51 (0.26), residues: 402 loop : -0.91 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP I 115 HIS 0.009 0.001 HIS I 45 PHE 0.014 0.001 PHE E 94 TYR 0.024 0.002 TYR C 164 ARG 0.006 0.000 ARG H 334 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 1313) hydrogen bonds : angle 5.26067 ( 3777) covalent geometry : bond 0.00308 (23898) covalent geometry : angle 0.61365 (32586) ********************** 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 344 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 2.521 Fit side-chains revert: symmetry clash REVERT: C 216 MET cc_start: 0.3125 (tmt) cc_final: 0.1844 (ppp) REVERT: A 69 ASN cc_start: 0.8913 (m-40) cc_final: 0.8620 (m110) REVERT: A 230 ASP cc_start: 0.8356 (t0) cc_final: 0.8120 (m-30) REVERT: A 251 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 7 GLU cc_start: 0.7963 (tp30) cc_final: 0.7635 (tm-30) REVERT: B 64 TRP cc_start: 0.8376 (m100) cc_final: 0.7758 (m100) REVERT: B 128 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7052 (pp) REVERT: B 211 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7281 (mtt-85) REVERT: I 7 GLU cc_start: 0.8124 (tp30) cc_final: 0.7807 (tm-30) REVERT: I 11 LYS cc_start: 0.7859 (tttt) cc_final: 0.7298 (tmmt) REVERT: F 5 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6477 (mtp85) REVERT: F 7 GLU cc_start: 0.7413 (pm20) cc_final: 0.6947 (tm-30) REVERT: F 11 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7383 (tmmt) REVERT: J 20 MET cc_start: 0.8039 (tmm) cc_final: 0.7762 (ttp) REVERT: J 62 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7547 (pm20) REVERT: J 83 LEU cc_start: 0.8359 (tt) cc_final: 0.7804 (tp) REVERT: J 156 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: J 214 TRP cc_start: 0.3267 (OUTLIER) cc_final: 0.3037 (p90) REVERT: G 20 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7066 (ttp) REVERT: G 62 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7628 (pm20) REVERT: G 83 LEU cc_start: 0.8314 (tt) cc_final: 0.7796 (tp) REVERT: G 101 ASN cc_start: 0.8642 (m110) cc_final: 0.8174 (m-40) REVERT: G 215 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.4131 (t80) REVERT: G 216 MET cc_start: 0.4937 (tmm) cc_final: 0.4454 (tmt) REVERT: H 381 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4283 (ptm) REVERT: E 230 ASP cc_start: 0.8184 (m-30) cc_final: 0.7842 (m-30) REVERT: E 251 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8202 (tt) REVERT: E 351 ASN cc_start: 0.8014 (p0) cc_final: 0.7792 (p0) REVERT: E 381 MET cc_start: 0.5594 (mmp) cc_final: 0.5187 (mmm) outliers start: 40 outliers final: 26 residues processed: 332 average time/residue: 1.4442 time to fit residues: 548.0937 Evaluate side-chains 329 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER 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 416 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 156 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 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 316 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 MET 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 277 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 21 HIS ** I 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117936 restraints weight = 25071.061| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.07 r_work: 0.3134 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 1.0209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23898 Z= 0.206 Angle : 0.698 10.517 32586 Z= 0.365 Chirality : 0.049 0.237 3450 Planarity : 0.006 0.078 4050 Dihedral : 5.049 44.576 3099 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 1.95 % Allowed : 25.17 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2826 helix: 1.21 (0.14), residues: 1419 sheet: 0.48 (0.26), residues: 402 loop : -0.99 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 115 HIS 0.010 0.001 HIS I 45 PHE 0.016 0.002 PHE C 228 TYR 0.033 0.002 TYR G 164 ARG 0.008 0.001 ARG H 334 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 1313) hydrogen bonds : angle 5.51693 ( 3777) covalent geometry : bond 0.00498 (23898) covalent geometry : angle 0.69811 (32586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17077.69 seconds wall clock time: 295 minutes 40.27 seconds (17740.27 seconds total)