Starting phenix.real_space_refine on Sat Jun 29 22:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vat_43102/06_2024/8vat_43102_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 Mg 3 5.21 5 S 105 5.16 5 Be 3 3.05 5 C 12098 2.51 5 N 3467 2.21 5 O 3697 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19423 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2828 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2878 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 17, 'TRANS': 352} Chain: "D" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2828 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2865 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 347} Chain: "G" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain: "H" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 8, 'rna3p': 2} Chain: "I" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3238 SG CYS B 64 75.938 75.504 112.483 1.00 66.96 S ATOM 3298 SG CYS B 73 79.605 75.311 112.680 1.00 83.13 S ATOM 3315 SG CYS B 76 78.875 72.860 111.723 1.00 78.73 S ATOM 3337 SG CYS B 79 77.214 73.571 109.402 1.00 67.06 S ATOM 6066 SG CYS C 64 90.770 43.355 81.922 1.00 47.62 S ATOM 6143 SG CYS C 76 88.632 40.388 79.926 1.00 63.98 S ATOM 6165 SG CYS C 79 87.154 42.658 79.361 1.00 61.59 S ATOM 8944 SG CYS D 64 59.665 23.588 52.604 1.00 54.67 S ATOM 9004 SG CYS D 73 58.229 21.365 49.904 1.00 57.03 S ATOM 9021 SG CYS D 76 56.935 21.029 53.491 1.00 75.55 S ATOM 9043 SG CYS D 79 55.920 23.917 51.850 1.00 63.33 S ATOM 11667 SG CYS E 50 17.543 41.276 52.102 1.00 76.32 S ATOM 11736 SG CYS E 59 14.467 38.989 51.712 1.00 98.26 S ATOM 11756 SG CYS E 62 16.530 38.681 54.688 1.00 95.62 S ATOM 11777 SG CYS E 65 14.423 41.639 54.506 1.00 89.97 S Time building chain proxies: 11.37, per 1000 atoms: 0.59 Number of scatterers: 19423 At special positions: 0 Unit cell: (106.48, 122.32, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 S 105 16.00 P 37 15.00 Mg 3 11.99 F 9 9.00 O 3697 8.00 N 3467 7.00 C 12098 6.00 Be 3 4.00 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 - 3.50 Amino acid : False - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 79 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 76 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 64 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 73 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 18 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 12 sheets defined 47.6% alpha, 12.6% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 removed outlier: 4.850A pdb=" N ARG A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 144 through 157 Proline residue: A 148 - end of helix Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 243 through 265 removed outlier: 3.853A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 280 through 290 removed outlier: 3.646A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.954A pdb=" N VAL A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.012A pdb=" N CYS A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'B' and resid 6 through 9 No H-bonds generated for 'chain 'B' and resid 6 through 9' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.738A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.679A pdb=" N ARG B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.586A pdb=" N GLN B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 278 through 297 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 304 through 319 removed outlier: 4.081A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 310 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 311 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 312 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 319 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'C' and resid 6 through 9 No H-bonds generated for 'chain 'C' and resid 6 through 9' Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.804A pdb=" N ALA C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 101 through 111 removed outlier: 3.580A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 133 through 144 removed outlier: 4.345A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 278 through 297 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 304 through 319 removed outlier: 5.192A pdb=" N ALA C 308 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU C 311 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 319 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 Proline residue: C 340 - end of helix Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'D' and resid 6 through 9 No H-bonds generated for 'chain 'D' and resid 6 through 9' Processing helix chain 'D' and resid 22 through 34 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 77 through 83 removed outlier: 3.680A pdb=" N GLU D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.010A pdb=" N ASN D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLN D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 133 through 144 removed outlier: 4.527A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 200 through 209 Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 278 through 297 Processing helix chain 'D' and resid 304 through 319 removed outlier: 4.586A pdb=" N ALA D 308 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU D 311 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 338 Processing helix chain 'D' and resid 345 through 357 Processing helix chain 'E' and resid 5 through 19 Proline residue: E 9 - end of helix removed outlier: 4.536A pdb=" N ALA E 16 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.739A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'E' and resid 169 through 179 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 208 through 226 removed outlier: 4.849A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 230 through 236 Processing helix chain 'E' and resid 241 through 259 Processing helix chain 'E' and resid 271 through 280 Processing helix chain 'E' and resid 283 through 302 Processing helix chain 'E' and resid 308 through 323 Processing helix chain 'F' and resid 11 through 18 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 132 through 140 Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 197 through 205 Processing helix chain 'F' and resid 244 through 247 No H-bonds generated for 'chain 'F' and resid 244 through 247' Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.642A pdb=" N ILE F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 321 through 330 Processing helix chain 'G' and resid 132 through 140 Processing helix chain 'G' and resid 143 through 145 No H-bonds generated for 'chain 'G' and resid 143 through 145' Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'G' and resid 244 through 247 No H-bonds generated for 'chain 'G' and resid 244 through 247' Processing helix chain 'G' and resid 260 through 273 removed outlier: 4.191A pdb=" N LEU G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 330 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.497A pdb=" N ALA A 20 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 137 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 22 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR A 21 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 110 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A 23 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL A 112 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN A 78 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE A 111 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 80 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG A 113 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 82 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 40 through 43 removed outlier: 8.707A pdb=" N TYR B 41 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 152 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE B 43 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 154 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 171 through 175 removed outlier: 8.971A pdb=" N TYR C 41 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE C 152 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE C 43 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 154 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY C 45 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR C 156 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 91 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 126 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 93 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 171 through 175 removed outlier: 8.843A pdb=" N TYR D 41 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE D 152 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE D 43 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 154 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY D 45 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR D 156 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 160 through 163 removed outlier: 8.397A pdb=" N LEU E 27 " --> pdb=" O THR E 139 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE E 141 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE E 29 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 143 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 3 through 5 Processing sheet with id= G, first strand: chain 'F' and resid 124 through 130 removed outlier: 6.816A pdb=" N ILE F 218 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU F 127 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL F 216 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR F 129 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU F 214 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN F 222 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 191 through 195 removed outlier: 3.608A pdb=" N GLN F 348 " --> pdb=" O MET F 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 289 through 294 Processing sheet with id= J, first strand: chain 'G' and resid 126 through 130 Processing sheet with id= K, first strand: chain 'G' and resid 191 through 196 removed outlier: 6.084A pdb=" N GLY G 157 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR G 172 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 315 through 320 removed outlier: 6.156A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6397 1.34 - 1.46: 3216 1.46 - 1.58: 9968 1.58 - 1.70: 74 1.70 - 1.82: 176 Bond restraints: 19831 Sorted by residual: bond pdb=" BE BEF D 403 " pdb=" F1 BEF D 403 " ideal model delta sigma weight residual 1.476 1.618 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" BE BEF C 403 " pdb=" F1 BEF C 403 " ideal model delta sigma weight residual 1.476 1.589 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" O3B ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 1.510 1.611 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O3B ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sigma weight residual 1.510 1.597 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" BE BEF D 403 " pdb=" F2 BEF D 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 19826 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.82: 618 105.82 - 113.23: 11186 113.23 - 120.64: 8471 120.64 - 128.05: 6575 128.05 - 135.46: 203 Bond angle restraints: 27053 Sorted by residual: angle pdb=" O2B ADP D 402 " pdb=" PB ADP D 402 " pdb=" O3B ADP D 402 " ideal model delta sigma weight residual 119.90 98.41 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" O2B ADP B 402 " pdb=" PB ADP B 402 " pdb=" O3B ADP B 402 " ideal model delta sigma weight residual 119.90 99.59 20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" O2B ADP C 402 " pdb=" PB ADP C 402 " pdb=" O3B ADP C 402 " ideal model delta sigma weight residual 119.90 101.81 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" F2 BEF C 403 " pdb=" BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.21 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N HIS G 175 " pdb=" CA HIS G 175 " pdb=" C HIS G 175 " ideal model delta sigma weight residual 114.56 109.26 5.30 1.27e+00 6.20e-01 1.74e+01 ... (remaining 27048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 10952 20.41 - 40.82: 827 40.82 - 61.23: 202 61.23 - 81.64: 59 81.64 - 102.05: 16 Dihedral angle restraints: 12056 sinusoidal: 5117 harmonic: 6939 Sorted by residual: dihedral pdb=" O1B ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " pdb=" PA ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 27.28 -87.28 1 2.00e+01 2.50e-03 2.29e+01 dihedral pdb=" O1B ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " pdb=" PA ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 26.96 -86.96 1 2.00e+01 2.50e-03 2.27e+01 dihedral pdb=" CA TYR C 41 " pdb=" C TYR C 41 " pdb=" N LEU C 42 " pdb=" CA LEU C 42 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2592 0.052 - 0.105: 463 0.105 - 0.157: 64 0.157 - 0.210: 5 0.210 - 0.262: 2 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C2' ADP D 402 " pdb=" C1' ADP D 402 " pdb=" C3' ADP D 402 " pdb=" O2' ADP D 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU F 42 " pdb=" CB LEU F 42 " pdb=" CD1 LEU F 42 " pdb=" CD2 LEU F 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3123 not shown) Planarity restraints: 3407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 360 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO D 361 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 41 " 0.032 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR C 41 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 41 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 41 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 41 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 41 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 41 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 41 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET G 182 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO G 183 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.032 5.00e-02 4.00e+02 ... (remaining 3404 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 37 2.35 - 2.99: 9867 2.99 - 3.62: 30271 3.62 - 4.26: 45774 4.26 - 4.90: 76204 Nonbonded interactions: 162153 Sorted by model distance: nonbonded pdb=" F1 BEF C 403 " pdb="MG MG C 404 " model vdw 1.709 2.120 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 404 " model vdw 1.818 2.170 nonbonded pdb=" O1B ADP C 402 " pdb="MG MG C 404 " model vdw 1.849 2.170 nonbonded pdb=" O1B ADP D 402 " pdb="MG MG D 404 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 404 " model vdw 1.992 2.170 ... (remaining 162148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid -2 through 361 or resid 401 through 404)) selection = chain 'D' } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 63.660 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 19831 Z= 0.325 Angle : 0.723 21.488 27053 Z= 0.338 Chirality : 0.041 0.262 3126 Planarity : 0.004 0.065 3407 Dihedral : 16.280 102.046 7554 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.18), residues: 2379 helix: 0.79 (0.15), residues: 1183 sheet: 0.03 (0.26), residues: 374 loop : -0.60 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 10 HIS 0.006 0.001 HIS B 0 PHE 0.021 0.002 PHE G 267 TYR 0.032 0.002 TYR C 41 ARG 0.004 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7713 (tt0) cc_final: 0.7413 (tt0) REVERT: A 252 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6685 (mtm-85) REVERT: B 318 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7334 (ptt-90) REVERT: C 160 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7508 (pm20) REVERT: C 328 TYR cc_start: 0.8536 (m-80) cc_final: 0.8084 (m-80) REVERT: D 41 TYR cc_start: 0.8840 (m-80) cc_final: 0.8631 (m-80) REVERT: D 256 MET cc_start: 0.8336 (tmm) cc_final: 0.8092 (ttp) REVERT: D 285 MET cc_start: 0.7763 (mtt) cc_final: 0.7451 (mtt) REVERT: D 306 MET cc_start: 0.6824 (ptm) cc_final: 0.6571 (ptm) REVERT: E 91 ASP cc_start: 0.7715 (m-30) cc_final: 0.7429 (m-30) REVERT: E 175 TRP cc_start: 0.6366 (t-100) cc_final: 0.6135 (t-100) REVERT: E 280 HIS cc_start: 0.6874 (t70) cc_final: 0.6469 (m-70) REVERT: F 1 MET cc_start: 0.7231 (ptt) cc_final: 0.7023 (ptp) REVERT: F 73 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6984 (mmm160) REVERT: F 201 ILE cc_start: 0.8453 (mt) cc_final: 0.8047 (pt) REVERT: G 254 LYS cc_start: 0.7547 (mppt) cc_final: 0.7291 (mmtp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3396 time to fit residues: 182.0562 Evaluate side-chains 259 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 4.9990 chunk 181 optimal weight: 0.0170 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN C 360 HIS D 182 GLN E 209 ASN E 287 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN G 186 GLN G 226 HIS ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19831 Z= 0.185 Angle : 0.590 9.458 27053 Z= 0.284 Chirality : 0.038 0.147 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.777 104.564 3033 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.63 % Rotamer: Outliers : 1.15 % Allowed : 7.86 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.18), residues: 2379 helix: 1.10 (0.15), residues: 1183 sheet: 0.14 (0.27), residues: 374 loop : -0.51 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.017 0.001 HIS C 360 PHE 0.014 0.001 PHE D 359 TYR 0.024 0.001 TYR C 41 ARG 0.006 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: A 252 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6677 (mtm-85) REVERT: B 318 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7339 (ptt-90) REVERT: C 160 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7465 (pm20) REVERT: C 192 ASN cc_start: 0.7244 (m110) cc_final: 0.6928 (m110) REVERT: D 306 MET cc_start: 0.6654 (ptm) cc_final: 0.6427 (ptm) REVERT: E 91 ASP cc_start: 0.7591 (m-30) cc_final: 0.7354 (m-30) REVERT: E 175 TRP cc_start: 0.6376 (t-100) cc_final: 0.6171 (t-100) REVERT: E 254 ASP cc_start: 0.7143 (m-30) cc_final: 0.6629 (m-30) REVERT: E 280 HIS cc_start: 0.6907 (t70) cc_final: 0.6506 (m-70) REVERT: F 201 ILE cc_start: 0.8435 (mt) cc_final: 0.8037 (pt) REVERT: G 254 LYS cc_start: 0.7601 (mppt) cc_final: 0.7310 (mmtp) outliers start: 23 outliers final: 13 residues processed: 301 average time/residue: 0.3332 time to fit residues: 148.4857 Evaluate side-chains 271 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 222 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 234 optimal weight: 0.2980 chunk 193 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN B 110 ASN C 192 ASN E 209 ASN E 307 ASN G 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19831 Z= 0.185 Angle : 0.563 8.150 27053 Z= 0.271 Chirality : 0.038 0.138 3126 Planarity : 0.004 0.049 3407 Dihedral : 13.482 106.200 3033 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.84 % Rotamer: Outliers : 2.00 % Allowed : 10.46 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.18), residues: 2379 helix: 1.20 (0.16), residues: 1185 sheet: 0.27 (0.27), residues: 367 loop : -0.44 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.005 0.001 HIS E 259 PHE 0.013 0.001 PHE D 359 TYR 0.026 0.001 TYR F 310 ARG 0.005 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 285 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7588 (mmt180) REVERT: A 194 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: A 252 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6740 (mtm-85) REVERT: B 34 LEU cc_start: 0.8333 (mp) cc_final: 0.8068 (mt) REVERT: C 160 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7387 (pm20) REVERT: E 91 ASP cc_start: 0.7526 (m-30) cc_final: 0.7298 (m-30) REVERT: E 280 HIS cc_start: 0.6892 (t70) cc_final: 0.6484 (m-70) REVERT: F 201 ILE cc_start: 0.8430 (mt) cc_final: 0.8060 (pt) REVERT: G 254 LYS cc_start: 0.7568 (mppt) cc_final: 0.7273 (mmtp) outliers start: 40 outliers final: 24 residues processed: 309 average time/residue: 0.3427 time to fit residues: 156.0144 Evaluate side-chains 284 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 0.0370 chunk 206 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN B 110 ASN B 182 GLN C 235 GLN C 360 HIS ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19831 Z= 0.170 Angle : 0.558 9.018 27053 Z= 0.267 Chirality : 0.037 0.142 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.328 105.881 3033 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.18), residues: 2379 helix: 1.27 (0.16), residues: 1195 sheet: 0.34 (0.27), residues: 362 loop : -0.42 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.008 0.001 HIS E 259 PHE 0.011 0.001 PHE F 319 TYR 0.035 0.001 TYR F 310 ARG 0.004 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7455 (mmt180) REVERT: A 252 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6679 (mtm-85) REVERT: C 160 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7323 (pm20) REVERT: C 333 LEU cc_start: 0.8622 (tt) cc_final: 0.8359 (tt) REVERT: D 204 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: D 251 SER cc_start: 0.8677 (t) cc_final: 0.8324 (p) REVERT: D 258 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: E 1 MET cc_start: 0.2194 (ppp) cc_final: 0.1577 (tpp) REVERT: E 91 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30) REVERT: E 254 ASP cc_start: 0.7114 (m-30) cc_final: 0.6632 (m-30) REVERT: E 318 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7557 (ttp-110) REVERT: F 182 MET cc_start: 0.6669 (mtt) cc_final: 0.6442 (mtt) REVERT: F 201 ILE cc_start: 0.8432 (mt) cc_final: 0.8056 (pt) REVERT: G 254 LYS cc_start: 0.7553 (mppt) cc_final: 0.7253 (mmtp) outliers start: 38 outliers final: 26 residues processed: 304 average time/residue: 0.3466 time to fit residues: 153.8690 Evaluate side-chains 290 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 235 GLN C 360 HIS ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 0 HIS F 222 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19831 Z= 0.359 Angle : 0.675 9.029 27053 Z= 0.323 Chirality : 0.042 0.166 3126 Planarity : 0.005 0.051 3407 Dihedral : 13.487 100.557 3033 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 3.00 % Allowed : 13.36 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.17), residues: 2379 helix: 0.81 (0.15), residues: 1190 sheet: 0.14 (0.27), residues: 367 loop : -0.65 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 229 HIS 0.008 0.001 HIS E 259 PHE 0.017 0.002 PHE D 15 TYR 0.022 0.002 TYR C 41 ARG 0.005 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7576 (mmt180) REVERT: A 96 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: A 252 ARG cc_start: 0.7292 (ttm110) cc_final: 0.6890 (mtm-85) REVERT: B 318 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7279 (ptt-90) REVERT: C 41 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5906 (p90) REVERT: C 160 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7465 (pm20) REVERT: D 204 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: D 258 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 1 MET cc_start: 0.2499 (ppp) cc_final: 0.2284 (mmt) REVERT: E 91 ASP cc_start: 0.7717 (m-30) cc_final: 0.7483 (m-30) REVERT: E 254 ASP cc_start: 0.7276 (m-30) cc_final: 0.6776 (m-30) REVERT: E 280 HIS cc_start: 0.6940 (t70) cc_final: 0.6547 (m-70) REVERT: E 292 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7488 (t0) REVERT: F 182 MET cc_start: 0.6913 (mtt) cc_final: 0.6544 (mtt) REVERT: F 201 ILE cc_start: 0.8397 (mt) cc_final: 0.8019 (pt) REVERT: G 201 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7614 (mm) REVERT: G 254 LYS cc_start: 0.7532 (mppt) cc_final: 0.7198 (mmtp) outliers start: 60 outliers final: 42 residues processed: 310 average time/residue: 0.3497 time to fit residues: 159.1396 Evaluate side-chains 301 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19831 Z= 0.195 Angle : 0.569 8.206 27053 Z= 0.274 Chirality : 0.038 0.144 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.206 100.960 3033 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.84 % Rotamer: Outliers : 2.10 % Allowed : 15.27 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.53 (0.18), residues: 2379 helix: 1.09 (0.16), residues: 1183 sheet: 0.19 (0.27), residues: 367 loop : -0.52 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.008 0.001 HIS E 259 PHE 0.014 0.001 PHE F 319 TYR 0.015 0.001 TYR F 284 ARG 0.006 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9089 (mt) cc_final: 0.8887 (mp) REVERT: A 252 ARG cc_start: 0.7218 (ttm110) cc_final: 0.6799 (mtm-85) REVERT: B 318 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7263 (ptt-90) REVERT: C 41 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.5666 (p90) REVERT: C 160 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7430 (pm20) REVERT: D 251 SER cc_start: 0.8702 (t) cc_final: 0.8307 (p) REVERT: D 258 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: E 88 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8377 (tt) REVERT: E 91 ASP cc_start: 0.7596 (m-30) cc_final: 0.7378 (m-30) REVERT: E 182 MET cc_start: 0.7103 (mtp) cc_final: 0.6857 (mtp) REVERT: E 254 ASP cc_start: 0.7181 (m-30) cc_final: 0.6687 (m-30) REVERT: E 280 HIS cc_start: 0.6937 (t70) cc_final: 0.6526 (m-70) REVERT: E 292 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7404 (t0) REVERT: F 182 MET cc_start: 0.6996 (mtt) cc_final: 0.6675 (mtt) REVERT: F 201 ILE cc_start: 0.8322 (mt) cc_final: 0.7977 (pt) REVERT: G 204 MET cc_start: 0.8213 (tpp) cc_final: 0.7948 (tpp) REVERT: G 254 LYS cc_start: 0.7561 (mppt) cc_final: 0.7221 (mmtp) outliers start: 42 outliers final: 29 residues processed: 298 average time/residue: 0.3389 time to fit residues: 149.8056 Evaluate side-chains 286 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.0370 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 110 ASN C 235 GLN C 360 HIS E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19831 Z= 0.201 Angle : 0.570 7.926 27053 Z= 0.273 Chirality : 0.038 0.138 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.027 99.893 3033 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.63 % Rotamer: Outliers : 2.65 % Allowed : 15.22 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.60 (0.18), residues: 2379 helix: 1.15 (0.16), residues: 1185 sheet: 0.20 (0.27), residues: 367 loop : -0.50 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 10 HIS 0.009 0.001 HIS E 259 PHE 0.012 0.001 PHE F 319 TYR 0.016 0.001 TYR C 41 ARG 0.007 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: B 318 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7237 (ptt-90) REVERT: C 41 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5681 (p90) REVERT: C 160 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7413 (pm20) REVERT: D 251 SER cc_start: 0.8694 (t) cc_final: 0.8286 (p) REVERT: D 258 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: E 88 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8367 (tt) REVERT: E 91 ASP cc_start: 0.7617 (m-30) cc_final: 0.7398 (m-30) REVERT: E 182 MET cc_start: 0.7012 (mtp) cc_final: 0.6758 (mtp) REVERT: E 254 ASP cc_start: 0.7175 (m-30) cc_final: 0.6700 (m-30) REVERT: E 292 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7442 (t0) REVERT: F 29 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7740 (mt) REVERT: F 182 MET cc_start: 0.6945 (mtt) cc_final: 0.6677 (mtt) REVERT: F 201 ILE cc_start: 0.8338 (mt) cc_final: 0.7996 (pt) REVERT: G 204 MET cc_start: 0.8142 (tpp) cc_final: 0.7939 (tpp) REVERT: G 254 LYS cc_start: 0.7540 (mppt) cc_final: 0.7207 (mmtp) outliers start: 53 outliers final: 38 residues processed: 299 average time/residue: 0.3313 time to fit residues: 148.1701 Evaluate side-chains 293 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 0.0370 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 146 optimal weight: 0.0570 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19831 Z= 0.160 Angle : 0.553 7.808 27053 Z= 0.266 Chirality : 0.037 0.142 3126 Planarity : 0.004 0.051 3407 Dihedral : 12.877 99.615 3033 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.36 % Favored : 96.51 % Rotamer: Outliers : 2.05 % Allowed : 15.97 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.18), residues: 2379 helix: 1.26 (0.16), residues: 1194 sheet: 0.26 (0.28), residues: 361 loop : -0.43 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 175 HIS 0.008 0.001 HIS E 259 PHE 0.009 0.001 PHE F 3 TYR 0.013 0.001 TYR F 284 ARG 0.006 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 45 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6543 (mp10) REVERT: A 238 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8568 (mm) REVERT: C 41 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5527 (p90) REVERT: C 160 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7415 (pm20) REVERT: D 251 SER cc_start: 0.8658 (t) cc_final: 0.8272 (p) REVERT: D 258 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: E 182 MET cc_start: 0.7040 (mtp) cc_final: 0.6789 (mtp) REVERT: E 254 ASP cc_start: 0.7094 (m-30) cc_final: 0.6605 (m-30) REVERT: F 1 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6771 (ptm) REVERT: F 29 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7711 (mt) REVERT: F 201 ILE cc_start: 0.8340 (mt) cc_final: 0.8005 (pt) REVERT: G 254 LYS cc_start: 0.7539 (mppt) cc_final: 0.7218 (mmtp) outliers start: 41 outliers final: 31 residues processed: 294 average time/residue: 0.3239 time to fit residues: 141.7177 Evaluate side-chains 290 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 214 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN G 226 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19831 Z= 0.267 Angle : 0.612 8.459 27053 Z= 0.292 Chirality : 0.040 0.143 3126 Planarity : 0.004 0.055 3407 Dihedral : 13.031 95.924 3033 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 2.80 % Allowed : 15.22 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.18), residues: 2379 helix: 1.03 (0.15), residues: 1190 sheet: 0.18 (0.27), residues: 367 loop : -0.52 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 229 HIS 0.009 0.001 HIS E 259 PHE 0.013 0.001 PHE F 319 TYR 0.019 0.002 TYR E 222 ARG 0.005 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 2.096 Fit side-chains REVERT: A 33 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 45 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6562 (mp10) REVERT: A 238 LEU cc_start: 0.8859 (mm) cc_final: 0.8494 (mm) REVERT: B 306 MET cc_start: 0.7959 (mtm) cc_final: 0.7635 (ptp) REVERT: C 41 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.5852 (p90) REVERT: C 160 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7443 (pm20) REVERT: D 251 SER cc_start: 0.8726 (t) cc_final: 0.8312 (p) REVERT: D 258 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: E 91 ASP cc_start: 0.7646 (m-30) cc_final: 0.7426 (m-30) REVERT: E 254 ASP cc_start: 0.7192 (m-30) cc_final: 0.6719 (m-30) REVERT: E 280 HIS cc_start: 0.6969 (t70) cc_final: 0.6529 (m-70) REVERT: F 14 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8234 (mp) REVERT: F 29 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7787 (mp) REVERT: F 201 ILE cc_start: 0.8384 (mt) cc_final: 0.8038 (pt) REVERT: F 315 MET cc_start: 0.4449 (ppp) cc_final: 0.4084 (tmm) REVERT: G 204 MET cc_start: 0.8194 (tpp) cc_final: 0.7240 (tpp) REVERT: G 254 LYS cc_start: 0.7528 (mppt) cc_final: 0.7154 (mmtp) outliers start: 56 outliers final: 38 residues processed: 296 average time/residue: 0.3314 time to fit residues: 146.9213 Evaluate side-chains 295 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 138 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 219 optimal weight: 0.0870 chunk 189 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19831 Z= 0.193 Angle : 0.583 9.581 27053 Z= 0.278 Chirality : 0.038 0.170 3126 Planarity : 0.004 0.052 3407 Dihedral : 12.937 95.631 3033 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 1.95 % Allowed : 16.42 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.57 (0.18), residues: 2379 helix: 1.08 (0.15), residues: 1201 sheet: 0.38 (0.28), residues: 357 loop : -0.55 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 175 HIS 0.010 0.001 HIS E 259 PHE 0.010 0.001 PHE F 3 TYR 0.014 0.001 TYR C 41 ARG 0.004 0.000 ARG E 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 45 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6549 (mp10) REVERT: A 143 GLU cc_start: 0.7364 (mp0) cc_final: 0.6913 (mt-10) REVERT: A 158 LEU cc_start: 0.9090 (mt) cc_final: 0.8888 (mp) REVERT: A 238 LEU cc_start: 0.8841 (mm) cc_final: 0.8503 (mm) REVERT: B 306 MET cc_start: 0.7919 (mtm) cc_final: 0.7635 (ptp) REVERT: C 41 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5637 (p90) REVERT: C 160 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7423 (pm20) REVERT: D 251 SER cc_start: 0.8673 (t) cc_final: 0.8286 (p) REVERT: D 258 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: E 254 ASP cc_start: 0.7160 (m-30) cc_final: 0.6686 (m-30) REVERT: F 1 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6880 (ptm) REVERT: F 14 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8142 (mp) REVERT: F 29 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7753 (mp) REVERT: F 51 MET cc_start: 0.8411 (mtp) cc_final: 0.8188 (mtm) REVERT: F 201 ILE cc_start: 0.8373 (mt) cc_final: 0.8033 (pt) REVERT: G 204 MET cc_start: 0.8149 (tpp) cc_final: 0.7247 (tpp) REVERT: G 254 LYS cc_start: 0.7534 (mppt) cc_final: 0.7208 (mmtp) outliers start: 39 outliers final: 30 residues processed: 290 average time/residue: 0.3188 time to fit residues: 139.3886 Evaluate side-chains 290 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.191313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161097 restraints weight = 24227.504| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.74 r_work: 0.3692 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19831 Z= 0.178 Angle : 0.573 9.962 27053 Z= 0.275 Chirality : 0.038 0.139 3126 Planarity : 0.004 0.052 3407 Dihedral : 12.855 95.146 3033 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 1.90 % Allowed : 17.07 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.66 (0.18), residues: 2379 helix: 1.13 (0.15), residues: 1204 sheet: 0.47 (0.28), residues: 349 loop : -0.50 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 175 HIS 0.010 0.001 HIS E 259 PHE 0.016 0.001 PHE F 319 TYR 0.013 0.001 TYR C 41 ARG 0.005 0.000 ARG G 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4236.15 seconds wall clock time: 75 minutes 49.90 seconds (4549.90 seconds total)