Starting phenix.real_space_refine on Sat Sep 28 11:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/09_2024/7quq_14151.cif" } resolution = 2.6 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= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3276 2.21 5 O 3615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19095 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "B" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "E" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "F" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.04, per 1000 atoms: 0.58 Number of scatterers: 19095 At special positions: 0 Unit cell: (71.74, 67.52, 270.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 18 15.00 O 3615 8.00 N 3276 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 3.3 seconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 51.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.614A pdb=" N SER A 51 " --> pdb=" O ASN A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 74 through 86 removed outlier: 4.497A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.932A pdb=" N GLY A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 145 through 163 Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.837A pdb=" N THR A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.000A pdb=" N ARG A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 246 removed outlier: 4.361A pdb=" N SER A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.585A pdb=" N GLU A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.811A pdb=" N GLU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 396 removed outlier: 4.071A pdb=" N ARG A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 409 through 428 Processing helix chain 'B' and resid 10 through 28 removed outlier: 4.327A pdb=" N ARG B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 removed outlier: 4.261A pdb=" N VAL B 50 " --> pdb=" O ASN B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.758A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.671A pdb=" N GLY B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.241A pdb=" N ARG B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.576A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.626A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.703A pdb=" N SER C 51 " --> pdb=" O ASN C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 74 through 86 removed outlier: 4.433A pdb=" N ILE C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.986A pdb=" N GLY C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 130 Proline residue: C 118 - end of helix Processing helix chain 'C' and resid 145 through 163 Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.910A pdb=" N THR C 195 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 4.009A pdb=" N ARG C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 246 removed outlier: 4.226A pdb=" N SER C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 310 through 314 removed outlier: 3.853A pdb=" N GLU C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 343 removed outlier: 3.535A pdb=" N GLU C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 394 removed outlier: 3.879A pdb=" N ARG C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.652A pdb=" N GLY C 407 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 428 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.970A pdb=" N ARG D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 removed outlier: 4.208A pdb=" N VAL D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 72 through 78 removed outlier: 4.057A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.776A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 3.669A pdb=" N GLY D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.156A pdb=" N ARG D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.649A pdb=" N SER D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 336 Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 425 removed outlier: 3.662A pdb=" N MET D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 31 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.686A pdb=" N SER E 51 " --> pdb=" O ASN E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 74 through 86 removed outlier: 4.529A pdb=" N ILE E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.942A pdb=" N GLY E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 Proline residue: E 118 - end of helix Processing helix chain 'E' and resid 145 through 163 Processing helix chain 'E' and resid 184 through 199 removed outlier: 3.735A pdb=" N THR E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.628A pdb=" N LEU E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.257A pdb=" N SER E 243 " --> pdb=" O GLY E 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.569A pdb=" N PHE E 300 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.771A pdb=" N GLU E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 343 removed outlier: 3.590A pdb=" N GLU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 396 removed outlier: 3.909A pdb=" N ARG E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 407 removed outlier: 3.818A pdb=" N GLY E 407 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.815A pdb=" N ARG F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 50 removed outlier: 4.331A pdb=" N VAL F 50 " --> pdb=" O ASN F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 110 through 127 removed outlier: 4.584A pdb=" N ASP F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.670A pdb=" N GLY F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.830A pdb=" N ASN F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.622A pdb=" N THR F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.695A pdb=" N PHE F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 330 through 336 Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 425 removed outlier: 3.658A pdb=" N MET F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 removed outlier: 7.975A pdb=" N ILE A 95 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 70 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASN A 5 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 136 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 142 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 169 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 137 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N CYS A 171 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 139 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 173 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N HIS A 141 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 168 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 204 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER A 170 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE A 206 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 172 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 203 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N CYS A 274 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 205 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N PHE A 276 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 13.628A pdb=" N ASP A 207 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 271 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 376 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 369 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR A 323 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 371 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 321 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 373 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A 319 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 375 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYS A 355 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 319 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY A 357 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 321 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 359 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR A 323 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.557A pdb=" N LEU B 5 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR B 137 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE B 7 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N SER B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE B 134 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE B 168 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 136 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 170 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N HIS B 138 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 200 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 268 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 202 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N PHE B 270 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 13.248A pdb=" N ASP B 204 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 265 " --> pdb=" O HIS B 371 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA B 315 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 368 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 313 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 94 through 96 removed outlier: 8.333A pdb=" N ILE C 95 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 70 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 5 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 138 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 7 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 9 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 169 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 137 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS C 171 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 139 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 173 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS C 141 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL C 168 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 204 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER C 170 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE C 206 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 172 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS C 203 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS C 274 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE C 205 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N PHE C 276 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 13.815A pdb=" N ASP C 207 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE C 271 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 376 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER C 369 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR C 323 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 371 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 321 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 373 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR C 319 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN C 375 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LYS C 355 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 319 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY C 357 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 321 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 359 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR C 323 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.679A pdb=" N VAL D 65 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLU D 3 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU D 5 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR D 137 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 7 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N SER D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL D 9 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN D 132 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE D 166 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE D 134 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 168 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET D 136 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL D 170 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N HIS D 138 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA D 200 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA D 268 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 202 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N PHE D 270 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N ASP D 204 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE D 265 " --> pdb=" O HIS D 371 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA D 315 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 368 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 313 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 96 removed outlier: 8.180A pdb=" N ILE E 95 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET E 70 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN E 5 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 136 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU E 169 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE E 137 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS E 171 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 139 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL E 173 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS E 141 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL E 168 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU E 204 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER E 170 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE E 206 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 172 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS E 203 " --> pdb=" O LEU E 272 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS E 274 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 205 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N PHE E 276 " --> pdb=" O ILE E 205 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 271 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 376 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER E 369 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 323 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 371 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 321 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU E 373 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR E 319 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN E 375 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LYS E 355 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 319 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY E 357 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL E 321 " --> pdb=" O GLY E 357 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL E 359 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR E 323 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'F' and resid 64 through 65 removed outlier: 6.677A pdb=" N LEU F 5 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR F 137 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE F 7 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N SER F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE F 134 " --> pdb=" O PHE F 166 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE F 168 " --> pdb=" O PHE F 134 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET F 136 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL F 170 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS F 138 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE F 165 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL F 201 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR F 167 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU F 203 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER F 169 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA F 200 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA F 268 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU F 202 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N PHE F 270 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 13.322A pdb=" N ASP F 204 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE F 265 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 52 through 54 904 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6287 1.34 - 1.46: 4434 1.46 - 1.59: 8584 1.59 - 1.71: 18 1.71 - 1.83: 162 Bond restraints: 19485 Sorted by residual: bond pdb=" C6 G2P D 501 " pdb=" O6 G2P D 501 " ideal model delta sigma weight residual 1.223 1.463 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C6 G2P F 501 " pdb=" O6 G2P F 501 " ideal model delta sigma weight residual 1.223 1.459 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C6 G2P B 501 " pdb=" O6 G2P B 501 " ideal model delta sigma weight residual 1.223 1.457 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C2' G2P D 501 " pdb=" C3' G2P D 501 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25839 2.49 - 4.99: 473 4.99 - 7.48: 97 7.48 - 9.97: 44 9.97 - 12.47: 19 Bond angle restraints: 26472 Sorted by residual: angle pdb=" C ASN D 298 " pdb=" N PHE D 299 " pdb=" CA PHE D 299 " ideal model delta sigma weight residual 120.71 126.27 -5.56 1.42e+00 4.96e-01 1.53e+01 angle pdb=" C ALA B 99 " pdb=" CA ALA B 99 " pdb=" CB ALA B 99 " ideal model delta sigma weight residual 115.79 111.14 4.65 1.19e+00 7.06e-01 1.53e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" N1 G2P E 501 " ideal model delta sigma weight residual 110.74 122.25 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C3A G2P F 501 " pdb=" PB G2P F 501 " pdb=" O3B G2P F 501 " ideal model delta sigma weight residual 99.71 110.75 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" O6 G2P E 501 " ideal model delta sigma weight residual 129.13 118.25 10.88 3.00e+00 1.11e-01 1.31e+01 ... (remaining 26467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 10572 17.36 - 34.72: 965 34.72 - 52.07: 133 52.07 - 69.43: 29 69.43 - 86.79: 22 Dihedral angle restraints: 11721 sinusoidal: 4677 harmonic: 7044 Sorted by residual: dihedral pdb=" CA TRP E 349 " pdb=" C TRP E 349 " pdb=" N ILE E 350 " pdb=" CA ILE E 350 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 369 " pdb=" C VAL B 369 " pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS D 163 " pdb=" C LYS D 163 " pdb=" N ARG D 164 " pdb=" CA ARG D 164 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2493 0.068 - 0.135: 447 0.135 - 0.203: 46 0.203 - 0.270: 5 0.270 - 0.338: 3 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CB ILE A 350 " pdb=" CA ILE A 350 " pdb=" CG1 ILE A 350 " pdb=" CG2 ILE A 350 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3' G2P C 501 " pdb=" C2' G2P C 501 " pdb=" C4' G2P C 501 " pdb=" O3' G2P C 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' G2P A 501 " pdb=" C2' G2P A 501 " pdb=" C4' G2P A 501 " pdb=" O3' G2P A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.43 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2991 not shown) Planarity restraints: 3399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 349 " -0.028 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP E 349 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 349 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 349 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 349 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 299 " 0.018 2.00e-02 2.50e+03 2.57e-02 1.16e+01 pdb=" CG PHE D 299 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D 299 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 299 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 182 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO F 183 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 183 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 183 " 0.043 5.00e-02 4.00e+02 ... (remaining 3396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 579 2.70 - 3.25: 19525 3.25 - 3.80: 34136 3.80 - 4.35: 45141 4.35 - 4.90: 72412 Nonbonded interactions: 171793 Sorted by model distance: nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 189 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 146 " pdb=" OG1 THR B 189 " model vdw 2.158 3.040 nonbonded pdb=" OG SER F 146 " pdb=" OG1 THR F 189 " model vdw 2.184 3.040 nonbonded pdb=" OG SER E 180 " pdb=" O LEU F 349 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASN E 188 " pdb=" OH TYR E 403 " model vdw 2.188 3.040 ... (remaining 171788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.550 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.009 0.240 19485 Z= 0.580 Angle : 0.938 12.467 26472 Z= 0.441 Chirality : 0.052 0.338 2994 Planarity : 0.006 0.077 3399 Dihedral : 13.757 86.788 7179 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.38 (0.16), residues: 2415 helix: -0.45 (0.15), residues: 1119 sheet: -0.36 (0.27), residues: 375 loop : -1.61 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP E 349 HIS 0.006 0.001 HIS E 141 PHE 0.058 0.002 PHE D 299 TYR 0.023 0.002 TYR F 422 ARG 0.007 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 481 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 MET cc_start: 0.6080 (mmt) cc_final: 0.5615 (mmp) REVERT: A 315 ARG cc_start: 0.5836 (tpp-160) cc_final: 0.4447 (ptt180) REVERT: A 354 PHE cc_start: 0.7904 (m-80) cc_final: 0.7513 (m-80) REVERT: B 88 GLU cc_start: 0.4830 (mp0) cc_final: 0.4558 (mp0) REVERT: B 193 ILE cc_start: 0.8040 (mt) cc_final: 0.7804 (mt) REVERT: C 403 TYR cc_start: 0.5373 (m-80) cc_final: 0.3917 (m-80) REVERT: D 88 GLU cc_start: 0.5457 (mp0) cc_final: 0.5218 (mp0) REVERT: D 299 PHE cc_start: 0.6615 (m-80) cc_final: 0.6201 (m-80) REVERT: E 219 TRP cc_start: 0.6205 (t-100) cc_final: 0.5990 (t-100) REVERT: E 245 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7125 (ttp80) REVERT: F 73 VAL cc_start: 0.6496 (p) cc_final: 0.5766 (t) REVERT: F 388 MET cc_start: 0.5143 (ptm) cc_final: 0.3943 (mmm) outliers start: 2 outliers final: 2 residues processed: 483 average time/residue: 1.1980 time to fit residues: 655.1948 Evaluate side-chains 274 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 304 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 263 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 401 ASN ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19485 Z= 0.298 Angle : 0.758 13.173 26472 Z= 0.379 Chirality : 0.050 0.371 2994 Planarity : 0.006 0.054 3399 Dihedral : 10.089 88.445 2824 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.40 % Rotamer: Outliers : 3.37 % Allowed : 14.04 % Favored : 82.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.41 % 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: -1.26 (0.16), residues: 2415 helix: -0.31 (0.15), residues: 1128 sheet: -0.46 (0.27), residues: 360 loop : -1.51 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 349 HIS 0.005 0.001 HIS D 8 PHE 0.038 0.002 PHE D 299 TYR 0.020 0.002 TYR C 323 ARG 0.006 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 315 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6602 (t) REVERT: A 244 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: A 312 MET cc_start: 0.6130 (mmt) cc_final: 0.5636 (mmp) REVERT: A 315 ARG cc_start: 0.6277 (tpp-160) cc_final: 0.4784 (ptt180) REVERT: B 70 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5695 (pp20) REVERT: B 398 TYR cc_start: 0.5777 (m-80) cc_final: 0.5347 (m-80) REVERT: D 76 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.5432 (mpp-170) REVERT: D 291 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.6071 (ptp-110) REVERT: D 299 PHE cc_start: 0.7166 (m-80) cc_final: 0.6694 (m-80) REVERT: E 244 MET cc_start: 0.7485 (mtm) cc_final: 0.6971 (mpp) REVERT: E 341 ARG cc_start: 0.6102 (ttp-110) cc_final: 0.5863 (tmm-80) REVERT: F 175 LEU cc_start: 0.7410 (pt) cc_final: 0.7193 (pp) REVERT: F 182 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6957 (pp20) REVERT: F 228 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8250 (mp) REVERT: F 388 MET cc_start: 0.5654 (ptm) cc_final: 0.3908 (mmt) outliers start: 68 outliers final: 22 residues processed: 364 average time/residue: 1.0862 time to fit residues: 453.5909 Evaluate side-chains 282 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 183 optimal weight: 0.0000 chunk 150 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 238 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 chunk 177 optimal weight: 0.0970 overall best weight: 0.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 16 ASN A 48 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN C 80 ASN D 53 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS E 90 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 247 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19485 Z= 0.201 Angle : 0.669 13.034 26472 Z= 0.333 Chirality : 0.046 0.231 2994 Planarity : 0.005 0.052 3399 Dihedral : 9.604 89.958 2820 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.08 % Allowed : 18.45 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.10 (0.17), residues: 2415 helix: -0.13 (0.15), residues: 1131 sheet: -0.55 (0.27), residues: 360 loop : -1.43 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 349 HIS 0.004 0.001 HIS F 8 PHE 0.023 0.001 PHE E 105 TYR 0.018 0.002 TYR C 163 ARG 0.010 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 296 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5866 (t80) cc_final: 0.5316 (t80) REVERT: A 312 MET cc_start: 0.6126 (mmt) cc_final: 0.5863 (mmt) REVERT: B 70 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5545 (pp20) REVERT: B 327 ASP cc_start: 0.7625 (m-30) cc_final: 0.7303 (m-30) REVERT: B 330 MET cc_start: 0.5214 (mmm) cc_final: 0.4901 (mpm) REVERT: B 355 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5222 (pm20) REVERT: B 398 TYR cc_start: 0.5601 (m-80) cc_final: 0.5259 (m-80) REVERT: D 291 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5755 (ptp-110) REVERT: D 299 PHE cc_start: 0.7089 (m-80) cc_final: 0.6661 (m-80) REVERT: D 382 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5291 (tp) REVERT: E 244 MET cc_start: 0.7422 (mtm) cc_final: 0.6980 (mpp) REVERT: E 341 ARG cc_start: 0.6110 (ttp-110) cc_final: 0.5818 (tmm-80) REVERT: F 137 THR cc_start: 0.7910 (p) cc_final: 0.7667 (p) REVERT: F 169 SER cc_start: 0.8827 (m) cc_final: 0.8532 (p) REVERT: F 175 LEU cc_start: 0.7407 (pt) cc_final: 0.7207 (pp) REVERT: F 228 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8245 (mp) REVERT: F 310 TYR cc_start: 0.7239 (m-80) cc_final: 0.6962 (m-80) REVERT: F 388 MET cc_start: 0.5494 (ptm) cc_final: 0.3673 (mmt) outliers start: 62 outliers final: 18 residues processed: 338 average time/residue: 1.0458 time to fit residues: 410.0647 Evaluate side-chains 268 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 210 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN B 247 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 185 ASN F 247 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19485 Z= 0.205 Angle : 0.654 12.472 26472 Z= 0.325 Chirality : 0.046 0.239 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.459 87.151 2820 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.62 % Allowed : 20.49 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.93 (0.17), residues: 2415 helix: 0.06 (0.15), residues: 1134 sheet: -0.69 (0.27), residues: 369 loop : -1.32 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 394 HIS 0.004 0.001 HIS A 270 PHE 0.029 0.002 PHE A 191 TYR 0.022 0.002 TYR F 106 ARG 0.012 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 279 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5755 (t80) cc_final: 0.5359 (t80) REVERT: A 312 MET cc_start: 0.6165 (mmt) cc_final: 0.5897 (mmt) REVERT: B 70 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5557 (pp20) REVERT: B 355 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5320 (pm20) REVERT: B 398 TYR cc_start: 0.5545 (m-80) cc_final: 0.5216 (m-80) REVERT: C 151 PHE cc_start: 0.6211 (t80) cc_final: 0.5966 (t80) REVERT: D 291 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5953 (ptp-110) REVERT: E 244 MET cc_start: 0.7518 (mtm) cc_final: 0.7126 (mpp) REVERT: E 341 ARG cc_start: 0.6131 (ttp-110) cc_final: 0.5904 (ttp80) REVERT: F 169 SER cc_start: 0.8737 (m) cc_final: 0.8522 (p) REVERT: F 224 ASP cc_start: 0.7432 (m-30) cc_final: 0.7227 (m-30) REVERT: F 228 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8217 (mp) REVERT: F 310 TYR cc_start: 0.7222 (m-80) cc_final: 0.6967 (m-80) REVERT: F 388 MET cc_start: 0.5466 (ptm) cc_final: 0.3872 (mmm) outliers start: 73 outliers final: 26 residues processed: 333 average time/residue: 1.0756 time to fit residues: 414.0504 Evaluate side-chains 269 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 264 HIS C 80 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN D 247 ASN D 298 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 19485 Z= 0.410 Angle : 0.830 13.322 26472 Z= 0.415 Chirality : 0.052 0.238 2994 Planarity : 0.006 0.053 3399 Dihedral : 10.193 82.034 2820 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 5.11 % Allowed : 21.28 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.34 (0.16), residues: 2415 helix: -0.23 (0.15), residues: 1131 sheet: -0.93 (0.28), residues: 327 loop : -1.56 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 219 HIS 0.008 0.002 HIS A 366 PHE 0.026 0.003 PHE D 299 TYR 0.036 0.003 TYR C 403 ARG 0.013 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 275 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: A 312 MET cc_start: 0.6452 (mmt) cc_final: 0.6032 (mmp) REVERT: A 315 ARG cc_start: 0.6627 (tpp-160) cc_final: 0.5369 (ptt180) REVERT: B 3 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4565 (mm-30) REVERT: B 112 LYS cc_start: 0.7380 (ptpp) cc_final: 0.7049 (ptpp) REVERT: B 176 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 355 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5705 (pm20) REVERT: B 398 TYR cc_start: 0.5909 (m-80) cc_final: 0.5447 (m-80) REVERT: C 151 PHE cc_start: 0.6691 (t80) cc_final: 0.6379 (t80) REVERT: D 90 SER cc_start: 0.4427 (m) cc_final: 0.3998 (p) REVERT: D 291 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6661 (ptp-110) REVERT: D 349 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7271 (mm) REVERT: E 74 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5694 (pt0) REVERT: E 178 GLN cc_start: 0.7781 (tt0) cc_final: 0.7575 (tt0) REVERT: E 341 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6195 (tmm-80) REVERT: F 158 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5744 (pm20) REVERT: F 228 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8564 (mp) REVERT: F 310 TYR cc_start: 0.7343 (m-80) cc_final: 0.7043 (m-80) REVERT: F 388 MET cc_start: 0.6053 (ptm) cc_final: 0.4345 (mmt) outliers start: 103 outliers final: 44 residues processed: 349 average time/residue: 1.1301 time to fit residues: 455.9251 Evaluate side-chains 284 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 407 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 400 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19485 Z= 0.239 Angle : 0.708 13.245 26472 Z= 0.350 Chirality : 0.047 0.193 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.649 75.847 2820 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.96 % Allowed : 23.02 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.14 (0.17), residues: 2415 helix: -0.06 (0.15), residues: 1134 sheet: -0.93 (0.26), residues: 369 loop : -1.45 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 102 HIS 0.005 0.001 HIS D 8 PHE 0.019 0.002 PHE E 105 TYR 0.024 0.002 TYR F 106 ARG 0.011 0.001 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6446 (tpp-160) cc_final: 0.5270 (ptt180) REVERT: B 112 LYS cc_start: 0.7319 (ptpp) cc_final: 0.6951 (pttp) REVERT: B 176 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 355 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5272 (pm20) REVERT: B 398 TYR cc_start: 0.5621 (m-80) cc_final: 0.5278 (m-80) REVERT: C 3 VAL cc_start: 0.7296 (m) cc_final: 0.7063 (p) REVERT: C 88 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5434 (tp) REVERT: C 151 PHE cc_start: 0.6532 (t80) cc_final: 0.6189 (t80) REVERT: D 291 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6330 (ptp-110) REVERT: E 341 ARG cc_start: 0.6421 (ttp-110) cc_final: 0.6095 (tmm-80) REVERT: F 100 ASN cc_start: 0.6167 (OUTLIER) cc_final: 0.5807 (m110) REVERT: F 158 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.5322 (pm20) REVERT: F 228 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (mp) REVERT: F 310 TYR cc_start: 0.7316 (m-80) cc_final: 0.7013 (m-80) REVERT: F 388 MET cc_start: 0.5841 (ptm) cc_final: 0.4326 (mmt) outliers start: 100 outliers final: 39 residues processed: 340 average time/residue: 0.9798 time to fit residues: 388.6341 Evaluate side-chains 271 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN B 400 ASN C 13 GLN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19485 Z= 0.233 Angle : 0.703 12.879 26472 Z= 0.347 Chirality : 0.047 0.187 2994 Planarity : 0.005 0.057 3399 Dihedral : 9.561 75.794 2820 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.22 % Allowed : 23.81 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.08 (0.17), residues: 2415 helix: 0.03 (0.15), residues: 1137 sheet: -1.03 (0.26), residues: 369 loop : -1.41 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 102 HIS 0.004 0.001 HIS D 8 PHE 0.021 0.002 PHE E 105 TYR 0.026 0.002 TYR C 403 ARG 0.015 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 255 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7696 (mtm) REVERT: B 26 ARG cc_start: 0.6437 (ppt170) cc_final: 0.6080 (ppt170) REVERT: B 176 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7601 (tp) REVERT: B 353 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: B 355 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5221 (pm20) REVERT: B 361 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.4482 (m-80) REVERT: B 398 TYR cc_start: 0.5602 (m-80) cc_final: 0.5268 (m-80) REVERT: C 3 VAL cc_start: 0.7289 (m) cc_final: 0.7078 (p) REVERT: C 88 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4989 (tp) REVERT: C 151 PHE cc_start: 0.6451 (t80) cc_final: 0.6140 (t80) REVERT: C 245 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6634 (mtp85) REVERT: D 291 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6293 (ptp-110) REVERT: E 341 ARG cc_start: 0.6377 (ttp-110) cc_final: 0.6053 (tmm-80) REVERT: F 160 TYR cc_start: 0.4798 (OUTLIER) cc_final: 0.3933 (m-10) REVERT: F 228 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (mp) REVERT: F 310 TYR cc_start: 0.7278 (m-80) cc_final: 0.6974 (m-80) REVERT: F 388 MET cc_start: 0.5707 (ptm) cc_final: 0.4274 (mmt) outliers start: 85 outliers final: 36 residues processed: 319 average time/residue: 1.0090 time to fit residues: 375.4966 Evaluate side-chains 266 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN B 100 ASN B 247 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19485 Z= 0.230 Angle : 0.704 12.736 26472 Z= 0.347 Chirality : 0.047 0.208 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.462 75.909 2820 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.82 % Allowed : 25.05 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.10 (0.17), residues: 2415 helix: 0.07 (0.15), residues: 1137 sheet: -1.00 (0.28), residues: 321 loop : -1.51 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 102 HIS 0.005 0.001 HIS F 8 PHE 0.018 0.001 PHE E 105 TYR 0.026 0.002 TYR C 403 ARG 0.012 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 248 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7750 (mtm) REVERT: B 286 PHE cc_start: 0.6264 (t80) cc_final: 0.6045 (t80) REVERT: B 355 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5225 (pm20) REVERT: B 398 TYR cc_start: 0.5505 (m-80) cc_final: 0.5254 (m-80) REVERT: C 3 VAL cc_start: 0.7284 (m) cc_final: 0.7079 (p) REVERT: C 88 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4685 (tt) REVERT: C 151 PHE cc_start: 0.6384 (t80) cc_final: 0.6053 (t80) REVERT: D 291 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6275 (ptp-110) REVERT: E 244 MET cc_start: 0.7618 (mtm) cc_final: 0.7164 (mpp) REVERT: E 341 ARG cc_start: 0.6358 (ttp-110) cc_final: 0.6041 (tmm-80) REVERT: F 31 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5323 (t) REVERT: F 158 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: F 160 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.3684 (m-10) REVERT: F 228 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8402 (mp) REVERT: F 310 TYR cc_start: 0.7232 (m-80) cc_final: 0.6958 (m-80) REVERT: F 388 MET cc_start: 0.5758 (ptm) cc_final: 0.4353 (mmt) REVERT: F 420 GLN cc_start: 0.5454 (pp30) cc_final: 0.5244 (pt0) outliers start: 77 outliers final: 42 residues processed: 302 average time/residue: 0.8918 time to fit residues: 314.0431 Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 206 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN B 247 ASN B 400 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19485 Z= 0.233 Angle : 0.719 12.791 26472 Z= 0.354 Chirality : 0.047 0.214 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.425 75.122 2820 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.52 % Allowed : 25.60 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.01 (0.17), residues: 2415 helix: 0.16 (0.16), residues: 1110 sheet: -1.06 (0.26), residues: 366 loop : -1.40 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 102 HIS 0.004 0.001 HIS D 8 PHE 0.024 0.002 PHE A 191 TYR 0.026 0.002 TYR F 106 ARG 0.010 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 245 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (mtm) REVERT: B 286 PHE cc_start: 0.6222 (t80) cc_final: 0.5960 (t80) REVERT: B 355 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5302 (pm20) REVERT: B 361 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.4412 (m-80) REVERT: B 398 TYR cc_start: 0.5488 (m-80) cc_final: 0.5237 (m-80) REVERT: C 3 VAL cc_start: 0.7285 (m) cc_final: 0.7074 (p) REVERT: C 88 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4632 (tt) REVERT: C 151 PHE cc_start: 0.6368 (t80) cc_final: 0.6031 (t80) REVERT: D 136 MET cc_start: 0.6818 (ttm) cc_final: 0.6495 (ttm) REVERT: D 291 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6232 (ptp-110) REVERT: E 244 MET cc_start: 0.7609 (mtm) cc_final: 0.7156 (mpp) REVERT: E 341 ARG cc_start: 0.6337 (ttp-110) cc_final: 0.6023 (tmm-80) REVERT: F 31 THR cc_start: 0.5800 (OUTLIER) cc_final: 0.5317 (t) REVERT: F 158 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5152 (pm20) REVERT: F 160 TYR cc_start: 0.4791 (OUTLIER) cc_final: 0.3312 (m-10) REVERT: F 228 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8393 (mp) REVERT: F 310 TYR cc_start: 0.7213 (m-80) cc_final: 0.6949 (m-80) REVERT: F 388 MET cc_start: 0.5762 (ptm) cc_final: 0.4363 (mmt) outliers start: 71 outliers final: 40 residues processed: 296 average time/residue: 0.9226 time to fit residues: 321.3023 Evaluate side-chains 276 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 247 ASN B 400 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19485 Z= 0.214 Angle : 0.709 12.785 26472 Z= 0.349 Chirality : 0.047 0.228 2994 Planarity : 0.005 0.054 3399 Dihedral : 9.211 75.243 2820 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.93 % Allowed : 26.59 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.98 (0.17), residues: 2415 helix: 0.19 (0.16), residues: 1110 sheet: -0.99 (0.28), residues: 318 loop : -1.43 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 102 HIS 0.004 0.001 HIS F 371 PHE 0.018 0.001 PHE D 166 TYR 0.032 0.002 TYR C 187 ARG 0.009 0.000 ARG C 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ARG cc_start: 0.6403 (ppt170) cc_final: 0.6160 (ppt170) REVERT: B 175 LEU cc_start: 0.7666 (pt) cc_final: 0.7440 (tp) REVERT: B 286 PHE cc_start: 0.6223 (t80) cc_final: 0.6014 (t80) REVERT: B 353 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7958 (m-10) REVERT: B 355 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: B 361 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.4269 (m-80) REVERT: C 88 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4484 (tt) REVERT: C 151 PHE cc_start: 0.6324 (t80) cc_final: 0.6008 (t80) REVERT: D 291 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6172 (ptp-110) REVERT: E 88 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.4412 (tp) REVERT: E 244 MET cc_start: 0.7547 (mtm) cc_final: 0.7181 (mpp) REVERT: E 341 ARG cc_start: 0.6290 (ttp-110) cc_final: 0.5981 (tmm-80) REVERT: F 31 THR cc_start: 0.5760 (OUTLIER) cc_final: 0.5304 (t) REVERT: F 160 TYR cc_start: 0.4821 (OUTLIER) cc_final: 0.2809 (m-10) REVERT: F 228 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8320 (mp) REVERT: F 388 MET cc_start: 0.5596 (ptm) cc_final: 0.4504 (mmt) outliers start: 59 outliers final: 38 residues processed: 301 average time/residue: 0.9785 time to fit residues: 343.8449 Evaluate side-chains 270 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 24 optimal weight: 0.0030 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 400 ASN C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.196822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.173714 restraints weight = 24405.834| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 1.89 r_work: 0.4399 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19485 Z= 0.260 Angle : 0.747 13.272 26472 Z= 0.368 Chirality : 0.048 0.278 2994 Planarity : 0.005 0.071 3399 Dihedral : 9.376 71.424 2820 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.83 % Allowed : 27.28 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.05 (0.17), residues: 2415 helix: 0.15 (0.16), residues: 1122 sheet: -1.00 (0.29), residues: 321 loop : -1.52 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 102 HIS 0.005 0.001 HIS F 8 PHE 0.028 0.002 PHE E 191 TYR 0.029 0.002 TYR C 187 ARG 0.016 0.001 ARG E 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6877.13 seconds wall clock time: 122 minutes 45.13 seconds (7365.13 seconds total)