Starting phenix.real_space_refine on Mon Jun 16 20:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_14151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_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/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_14151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_14151.map" model { file = "/net/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_14151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7quq_14151/06_2025/7quq_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-5710/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: 11.09, 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: 5.08 Conformation dependent library (CDL) restraints added in 2.3 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: 2.17 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: 5.97 Time building geometry restraints manager: 5.49 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: 0.03 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: 2.620 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: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.350 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.770 ------------------------------------------------------------------------------- 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 19494 Z= 0.447 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 Details of bonding type rmsd hydrogen bonds : bond 0.16562 ( 904) hydrogen bonds : angle 7.41342 ( 2682) covalent geometry : bond 0.00904 (19485) covalent geometry : angle 0.93760 (26472) Misc. bond : bond 0.00301 ( 9) *********************** 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 to be fit. rotamer outliers: 2 poor density : 481 time to evaluate : 2.183 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: 1.2363 time to fit residues: 677.4059 Evaluate side-chains 274 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.200305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.176110 restraints weight = 24123.555| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 1.90 r_work: 0.4419 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4294 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 19494 Z= 0.204 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 Details of bonding type rmsd hydrogen bonds : bond 0.05626 ( 904) hydrogen bonds : angle 5.86267 ( 2682) covalent geometry : bond 0.00459 (19485) covalent geometry : angle 0.75818 (26472) Misc. bond : bond 0.00452 ( 9) *********************** 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 to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7964 (pp20) cc_final: 0.7753 (pm20) REVERT: A 244 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: A 312 MET cc_start: 0.6686 (mmt) cc_final: 0.6207 (mmp) REVERT: A 315 ARG cc_start: 0.6489 (tpp-160) cc_final: 0.4706 (ptt180) REVERT: B 70 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6034 (pp20) REVERT: B 88 GLU cc_start: 0.4716 (mp0) cc_final: 0.4485 (mp0) REVERT: B 398 TYR cc_start: 0.5881 (m-80) cc_final: 0.5445 (m-80) REVERT: D 76 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5914 (mpp-170) REVERT: D 291 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6398 (ptp-110) REVERT: D 299 PHE cc_start: 0.7229 (m-80) cc_final: 0.6765 (m-80) REVERT: E 244 MET cc_start: 0.7708 (mtm) cc_final: 0.7257 (mpp) REVERT: E 341 ARG cc_start: 0.6514 (ttp-110) cc_final: 0.5920 (tmm-80) REVERT: F 129 LYS cc_start: 0.5292 (mppt) cc_final: 0.5043 (mppt) REVERT: F 175 LEU cc_start: 0.7548 (pt) cc_final: 0.7344 (pp) REVERT: F 182 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: F 184 TYR cc_start: 0.6857 (m-10) cc_final: 0.6622 (m-10) REVERT: F 228 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (mp) REVERT: F 388 MET cc_start: 0.5936 (ptm) cc_final: 0.3895 (mmt) outliers start: 68 outliers final: 22 residues processed: 364 average time/residue: 1.0758 time to fit residues: 450.4360 Evaluate side-chains 283 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** 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 F 247 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.200752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.175311 restraints weight = 24099.393| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 2.09 r_work: 0.4412 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19494 Z= 0.162 Angle : 0.688 13.391 26472 Z= 0.344 Chirality : 0.047 0.234 2994 Planarity : 0.005 0.051 3399 Dihedral : 9.762 88.560 2820 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.37 % Allowed : 18.40 % Favored : 78.22 % 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: -1.12 (0.17), residues: 2415 helix: -0.15 (0.15), residues: 1131 sheet: -0.54 (0.27), residues: 360 loop : -1.45 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 349 HIS 0.004 0.001 HIS F 8 PHE 0.024 0.002 PHE D 299 TYR 0.016 0.002 TYR D 342 ARG 0.011 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 904) hydrogen bonds : angle 5.64633 ( 2682) covalent geometry : bond 0.00364 (19485) covalent geometry : angle 0.68779 (26472) Misc. bond : bond 0.00422 ( 9) *********************** 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 363 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6016 (t80) cc_final: 0.5409 (t80) REVERT: A 244 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7822 (mtm) REVERT: A 312 MET cc_start: 0.6521 (mmt) cc_final: 0.6033 (mmp) REVERT: A 315 ARG cc_start: 0.6378 (tpp-160) cc_final: 0.4834 (ptt180) REVERT: B 70 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5662 (pp20) REVERT: B 330 MET cc_start: 0.5582 (mmm) cc_final: 0.5286 (mpm) REVERT: B 355 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5394 (pm20) REVERT: B 398 TYR cc_start: 0.5746 (m-80) cc_final: 0.5411 (m-80) REVERT: C 3 VAL cc_start: 0.7521 (m) cc_final: 0.7253 (p) REVERT: D 76 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5987 (mpp-170) REVERT: D 291 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6192 (ptp-110) REVERT: E 341 ARG cc_start: 0.6468 (ttp-110) cc_final: 0.5889 (tmm-80) REVERT: F 169 SER cc_start: 0.9001 (m) cc_final: 0.8739 (p) REVERT: F 175 LEU cc_start: 0.7619 (pt) cc_final: 0.7417 (pp) REVERT: F 224 ASP cc_start: 0.7720 (m-30) cc_final: 0.7473 (m-30) REVERT: F 228 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8367 (mp) REVERT: F 310 TYR cc_start: 0.7327 (m-80) cc_final: 0.7120 (m-80) REVERT: F 320 ASP cc_start: 0.7345 (t70) cc_final: 0.7131 (t0) REVERT: F 388 MET cc_start: 0.5774 (ptm) cc_final: 0.3741 (mmt) outliers start: 68 outliers final: 20 residues processed: 342 average time/residue: 1.3878 time to fit residues: 549.9478 Evaluate side-chains 269 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 244 MET 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 50 VAL Chi-restraints excluded: chain D residue 76 ARG 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 E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE 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 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 113 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 338 ASN C 13 GLN C 80 ASN D 15 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 298 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 247 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.194450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.170661 restraints weight = 24662.587| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.94 r_work: 0.4362 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19494 Z= 0.211 Angle : 0.744 12.659 26472 Z= 0.372 Chirality : 0.049 0.239 2994 Planarity : 0.005 0.051 3399 Dihedral : 9.977 83.530 2820 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.11 % Rotamer: Outliers : 4.86 % Allowed : 20.78 % Favored : 74.36 % 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: -1.20 (0.17), residues: 2415 helix: -0.13 (0.15), residues: 1134 sheet: -0.85 (0.29), residues: 318 loop : -1.48 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 219 HIS 0.005 0.001 HIS F 371 PHE 0.031 0.002 PHE A 191 TYR 0.026 0.003 TYR C 403 ARG 0.011 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 904) hydrogen bonds : angle 5.68584 ( 2682) covalent geometry : bond 0.00475 (19485) covalent geometry : angle 0.74437 (26472) Misc. bond : bond 0.00515 ( 9) *********************** 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 380 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 282 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7763 (mtm) REVERT: A 312 MET cc_start: 0.6585 (mmt) cc_final: 0.6359 (mmt) REVERT: A 315 ARG cc_start: 0.6650 (tpp-160) cc_final: 0.5268 (ptt180) REVERT: B 112 LYS cc_start: 0.7288 (ptpp) cc_final: 0.6967 (ptpp) REVERT: B 355 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5503 (pm20) REVERT: B 398 TYR cc_start: 0.5769 (m-80) cc_final: 0.5421 (m-80) REVERT: D 76 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5892 (mpp-170) REVERT: D 184 TYR cc_start: 0.7121 (m-10) cc_final: 0.6870 (m-10) REVERT: D 291 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6521 (ptp-110) REVERT: E 74 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5839 (pt0) REVERT: E 341 ARG cc_start: 0.6707 (ttp-110) cc_final: 0.6159 (tmm-80) REVERT: E 408 MET cc_start: 0.6564 (mtp) cc_final: 0.6324 (mtm) REVERT: F 182 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: F 224 ASP cc_start: 0.7563 (m-30) cc_final: 0.7312 (m-30) REVERT: F 228 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8672 (mp) REVERT: F 388 MET cc_start: 0.5832 (ptm) cc_final: 0.4031 (mmt) outliers start: 98 outliers final: 38 residues processed: 350 average time/residue: 1.1988 time to fit residues: 484.8912 Evaluate side-chains 284 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 TRP 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 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 C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 110 LEU 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 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL 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 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 74 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 229 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 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 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 229 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 239 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS E 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.197652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.173894 restraints weight = 24620.285| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.97 r_work: 0.4395 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19494 Z= 0.157 Angle : 0.687 12.616 26472 Z= 0.340 Chirality : 0.047 0.231 2994 Planarity : 0.005 0.054 3399 Dihedral : 9.632 80.525 2820 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.71 % Allowed : 22.72 % Favored : 72.57 % 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: 0.03 (0.15), residues: 1137 sheet: -0.88 (0.26), residues: 369 loop : -1.41 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 102 HIS 0.005 0.001 HIS F 8 PHE 0.018 0.002 PHE E 105 TYR 0.024 0.002 TYR A 403 ARG 0.013 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 904) hydrogen bonds : angle 5.49459 ( 2682) covalent geometry : bond 0.00357 (19485) covalent geometry : angle 0.68735 (26472) Misc. bond : bond 0.00374 ( 9) *********************** 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 367 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 272 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7825 (mtm) REVERT: A 315 ARG cc_start: 0.6599 (tpp-160) cc_final: 0.5221 (ptt180) REVERT: B 112 LYS cc_start: 0.7360 (ptpp) cc_final: 0.6959 (pttp) REVERT: B 355 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5328 (pm20) REVERT: B 361 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: B 398 TYR cc_start: 0.5547 (m-80) cc_final: 0.5242 (m-80) REVERT: C 3 VAL cc_start: 0.7428 (m) cc_final: 0.7175 (p) REVERT: D 76 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5766 (mpp-170) REVERT: D 273 MET cc_start: 0.4885 (OUTLIER) cc_final: 0.3920 (mpp) REVERT: D 291 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6386 (ptp-110) REVERT: E 74 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5622 (pt0) REVERT: E 244 MET cc_start: 0.7923 (mtm) cc_final: 0.7558 (mpp) REVERT: E 341 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.6100 (tmm-80) REVERT: F 206 GLU cc_start: 0.7472 (tt0) cc_final: 0.7208 (tp30) REVERT: F 224 ASP cc_start: 0.7646 (m-30) cc_final: 0.7380 (m-30) REVERT: F 228 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8646 (mp) REVERT: F 310 TYR cc_start: 0.7567 (m-80) cc_final: 0.7211 (m-80) REVERT: F 388 MET cc_start: 0.6001 (ptm) cc_final: 0.4058 (mmt) outliers start: 95 outliers final: 33 residues processed: 341 average time/residue: 0.9987 time to fit residues: 395.3413 Evaluate side-chains 278 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 23 LEU 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 B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 371 VAL 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 219 SER Chi-restraints excluded: chain D residue 273 MET 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 74 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 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 148 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 102 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** B 100 ASN B 247 ASN C 80 ASN ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.196700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.172882 restraints weight = 24567.083| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.99 r_work: 0.4380 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19494 Z= 0.171 Angle : 0.699 12.451 26472 Z= 0.346 Chirality : 0.047 0.198 2994 Planarity : 0.005 0.052 3399 Dihedral : 9.649 79.323 2820 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.76 % Allowed : 23.12 % Favored : 72.12 % 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: -1.14 (0.27), residues: 348 loop : -1.46 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 102 HIS 0.004 0.001 HIS F 371 PHE 0.024 0.002 PHE A 191 TYR 0.025 0.002 TYR C 403 ARG 0.012 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 904) hydrogen bonds : angle 5.49825 ( 2682) covalent geometry : bond 0.00390 (19485) covalent geometry : angle 0.69862 (26472) Misc. bond : bond 0.00412 ( 9) *********************** 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 347 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 251 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.7371 (ptpp) cc_final: 0.6965 (pttp) REVERT: B 355 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5220 (pm20) REVERT: B 361 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.4513 (m-80) REVERT: B 398 TYR cc_start: 0.5603 (m-80) cc_final: 0.5305 (m-80) REVERT: C 3 VAL cc_start: 0.7369 (m) cc_final: 0.7121 (p) REVERT: D 273 MET cc_start: 0.4671 (OUTLIER) cc_final: 0.3712 (mpp) REVERT: D 291 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6488 (ptp-110) REVERT: E 244 MET cc_start: 0.7928 (mtm) cc_final: 0.7552 (mpp) REVERT: E 340 MET cc_start: 0.5136 (ttp) cc_final: 0.4931 (tpp) REVERT: E 341 ARG cc_start: 0.6647 (ttp-110) cc_final: 0.6134 (tmm-80) REVERT: E 403 TYR cc_start: 0.5994 (m-80) cc_final: 0.4929 (m-80) REVERT: F 224 ASP cc_start: 0.7620 (m-30) cc_final: 0.7347 (m-30) REVERT: F 228 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8660 (mp) REVERT: F 310 TYR cc_start: 0.7557 (m-80) cc_final: 0.7232 (m-80) REVERT: F 388 MET cc_start: 0.6031 (ptm) cc_final: 0.4251 (mmt) outliers start: 96 outliers final: 40 residues processed: 321 average time/residue: 0.9471 time to fit residues: 356.1733 Evaluate side-chains 271 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 289 LEU 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 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 183 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 379 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 273 MET 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 166 ILE Chi-restraints excluded: chain E residue 182 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 F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 203 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.196709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.172672 restraints weight = 24317.742| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.94 r_work: 0.4397 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19494 Z= 0.159 Angle : 0.692 12.397 26472 Z= 0.343 Chirality : 0.046 0.182 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.567 77.773 2820 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.07 % Allowed : 24.31 % Favored : 71.63 % 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: -1.03 (0.17), residues: 2415 helix: 0.11 (0.15), residues: 1137 sheet: -1.01 (0.27), residues: 366 loop : -1.43 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 102 HIS 0.004 0.001 HIS F 8 PHE 0.027 0.002 PHE A 191 TYR 0.028 0.002 TYR C 403 ARG 0.012 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 904) hydrogen bonds : angle 5.44143 ( 2682) covalent geometry : bond 0.00362 (19485) covalent geometry : angle 0.69230 (26472) Misc. bond : bond 0.00387 ( 9) *********************** 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 336 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: B 112 LYS cc_start: 0.7316 (ptpp) cc_final: 0.6928 (pttp) REVERT: B 353 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: B 355 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5356 (pm20) REVERT: B 361 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: B 398 TYR cc_start: 0.5568 (m-80) cc_final: 0.5261 (m-80) REVERT: C 3 VAL cc_start: 0.7350 (m) cc_final: 0.7117 (p) REVERT: D 273 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.3636 (mpp) REVERT: D 291 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6495 (ptp-110) REVERT: E 244 MET cc_start: 0.7904 (mtm) cc_final: 0.7548 (mpp) REVERT: E 341 ARG cc_start: 0.6692 (ttp-110) cc_final: 0.6176 (tmm-80) REVERT: F 158 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.5414 (pm20) REVERT: F 160 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4092 (m-10) REVERT: F 184 TYR cc_start: 0.6320 (m-10) cc_final: 0.6091 (m-10) REVERT: F 224 ASP cc_start: 0.7589 (m-30) cc_final: 0.7312 (m-30) REVERT: F 228 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8654 (mp) REVERT: F 310 TYR cc_start: 0.7400 (m-80) cc_final: 0.7198 (m-80) REVERT: F 388 MET cc_start: 0.6086 (ptm) cc_final: 0.4310 (mmt) outliers start: 82 outliers final: 41 residues processed: 310 average time/residue: 0.9601 time to fit residues: 350.8098 Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 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 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 LEU 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 183 VAL 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 371 VAL Chi-restraints excluded: chain C residue 379 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 273 MET Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG 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 182 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 116 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 C 80 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.190656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.167239 restraints weight = 24733.640| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 1.91 r_work: 0.4334 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19494 Z= 0.234 Angle : 0.782 12.934 26472 Z= 0.389 Chirality : 0.050 0.275 2994 Planarity : 0.006 0.064 3399 Dihedral : 9.905 78.134 2820 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 4.02 % Allowed : 25.50 % 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: -1.27 (0.17), residues: 2415 helix: -0.10 (0.15), residues: 1137 sheet: -1.08 (0.29), residues: 318 loop : -1.56 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 23 HIS 0.005 0.001 HIS F 8 PHE 0.033 0.002 PHE A 191 TYR 0.041 0.003 TYR C 403 ARG 0.019 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.05216 ( 904) hydrogen bonds : angle 5.68005 ( 2682) covalent geometry : bond 0.00536 (19485) covalent geometry : angle 0.78225 (26472) Misc. bond : bond 0.00547 ( 9) *********************** 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 336 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 255 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: B 26 ARG cc_start: 0.6649 (pmt-80) cc_final: 0.6447 (pmt-80) REVERT: B 353 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: B 355 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5491 (pm20) REVERT: B 398 TYR cc_start: 0.5891 (m-80) cc_final: 0.5364 (m-80) REVERT: C 428 GLN cc_start: 0.4613 (OUTLIER) cc_final: 0.4266 (mm-40) REVERT: D 76 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.5801 (mpp-170) REVERT: D 223 MET cc_start: 0.7341 (mmp) cc_final: 0.7085 (mmp) REVERT: D 273 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.3666 (mpp) REVERT: D 291 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6858 (ptp-110) REVERT: E 244 MET cc_start: 0.8085 (mtm) cc_final: 0.7758 (mpp) REVERT: E 341 ARG cc_start: 0.6957 (ttp-110) cc_final: 0.6320 (tmm-80) REVERT: F 158 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.5317 (pm20) REVERT: F 160 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4454 (m-80) REVERT: F 184 TYR cc_start: 0.6542 (m-10) cc_final: 0.6276 (m-10) REVERT: F 224 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: F 228 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8763 (mp) REVERT: F 388 MET cc_start: 0.6256 (ptm) cc_final: 0.4549 (mmt) outliers start: 81 outliers final: 40 residues processed: 310 average time/residue: 1.0631 time to fit residues: 382.9806 Evaluate side-chains 278 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 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 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 LEU 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 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 251 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 VAL 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 273 MET Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 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 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 224 ASP 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 155 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 133 ASN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN 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 = 0.196422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.173648 restraints weight = 24649.323| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.89 r_work: 0.4390 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19494 Z= 0.160 Angle : 0.726 12.728 26472 Z= 0.357 Chirality : 0.047 0.201 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.543 70.194 2820 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.32 % Allowed : 26.59 % Favored : 70.09 % 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: -1.18 (0.17), residues: 2415 helix: 0.04 (0.15), residues: 1122 sheet: -1.09 (0.28), residues: 321 loop : -1.58 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 23 HIS 0.007 0.001 HIS F 8 PHE 0.031 0.002 PHE A 191 TYR 0.026 0.002 TYR C 403 ARG 0.013 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 904) hydrogen bonds : angle 5.51218 ( 2682) covalent geometry : bond 0.00364 (19485) covalent geometry : angle 0.72580 (26472) Misc. bond : bond 0.00377 ( 9) *********************** 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 327 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7675 (p) REVERT: B 355 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5365 (pm20) REVERT: B 398 TYR cc_start: 0.5576 (m-80) cc_final: 0.5317 (m-80) REVERT: C 3 VAL cc_start: 0.7326 (m) cc_final: 0.7101 (p) REVERT: C 376 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6838 (t0) REVERT: D 76 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5744 (mpp-170) REVERT: D 291 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6592 (ptp-110) REVERT: E 191 PHE cc_start: 0.6740 (m-10) cc_final: 0.6218 (m-10) REVERT: E 244 MET cc_start: 0.7893 (mtm) cc_final: 0.7483 (mpp) REVERT: E 341 ARG cc_start: 0.6603 (ttp-110) cc_final: 0.6131 (tmm-80) REVERT: E 403 TYR cc_start: 0.5979 (m-80) cc_final: 0.4803 (m-80) REVERT: F 31 THR cc_start: 0.5829 (OUTLIER) cc_final: 0.5367 (t) REVERT: F 158 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5310 (pm20) REVERT: F 160 TYR cc_start: 0.4817 (OUTLIER) cc_final: 0.3951 (m-80) REVERT: F 224 ASP cc_start: 0.7553 (m-30) cc_final: 0.7273 (m-30) REVERT: F 228 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8606 (mp) REVERT: F 388 MET cc_start: 0.6065 (ptm) cc_final: 0.4311 (mmt) REVERT: F 420 GLN cc_start: 0.5630 (pp30) cc_final: 0.5419 (pt0) outliers start: 67 outliers final: 34 residues processed: 305 average time/residue: 1.0820 time to fit residues: 389.6113 Evaluate side-chains 280 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 2.013 ------------------------------------------------------------------------------- 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 249 PHE Chi-restraints excluded: chain A residue 371 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 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 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 379 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 9 VAL 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 291 ARG Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN 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 Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 160 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 196 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 247 ASN B 400 ASN C 80 ASN D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.198270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.175307 restraints weight = 24533.261| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 1.88 r_work: 0.4413 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4291 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19494 Z= 0.153 Angle : 0.713 11.885 26472 Z= 0.352 Chirality : 0.047 0.215 2994 Planarity : 0.005 0.052 3399 Dihedral : 9.348 68.723 2820 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 27.88 % Favored : 69.44 % 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: -1.12 (0.17), residues: 2415 helix: 0.09 (0.16), residues: 1122 sheet: -1.17 (0.28), residues: 321 loop : -1.49 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 102 HIS 0.006 0.001 HIS F 8 PHE 0.032 0.001 PHE A 191 TYR 0.026 0.002 TYR F 106 ARG 0.012 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 904) hydrogen bonds : angle 5.42389 ( 2682) covalent geometry : bond 0.00349 (19485) covalent geometry : angle 0.71307 (26472) Misc. bond : bond 0.00343 ( 9) ********************** 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 306 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 HIS cc_start: 0.7166 (p-80) cc_final: 0.6913 (p90) REVERT: B 175 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7598 (tp) REVERT: B 353 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: B 355 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5032 (pm20) REVERT: B 398 TYR cc_start: 0.5510 (m-80) cc_final: 0.5207 (m-80) REVERT: C 3 VAL cc_start: 0.7356 (m) cc_final: 0.7130 (p) REVERT: C 110 LEU cc_start: 0.6571 (mm) cc_final: 0.6296 (mm) REVERT: C 364 ILE cc_start: 0.7504 (mm) cc_final: 0.7303 (mt) REVERT: C 376 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6769 (t0) REVERT: D 76 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5829 (mpp-170) REVERT: D 247 ASN cc_start: 0.6443 (m-40) cc_final: 0.6242 (m110) REVERT: D 291 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6651 (ptp-110) REVERT: D 420 GLN cc_start: 0.5302 (pt0) cc_final: 0.4923 (tp-100) REVERT: E 191 PHE cc_start: 0.6807 (m-10) cc_final: 0.6296 (m-10) REVERT: E 209 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: E 244 MET cc_start: 0.7985 (mtm) cc_final: 0.7613 (mpp) REVERT: E 341 ARG cc_start: 0.6786 (ttp-110) cc_final: 0.6214 (tmm-80) REVERT: E 403 TYR cc_start: 0.5818 (m-80) cc_final: 0.4531 (m-80) REVERT: F 31 THR cc_start: 0.5805 (OUTLIER) cc_final: 0.5346 (t) REVERT: F 160 TYR cc_start: 0.4888 (OUTLIER) cc_final: 0.3402 (m-10) REVERT: F 184 TYR cc_start: 0.6309 (m-10) cc_final: 0.6015 (m-10) REVERT: F 224 ASP cc_start: 0.7517 (m-30) cc_final: 0.7211 (m-30) REVERT: F 228 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8640 (mp) REVERT: F 388 MET cc_start: 0.6386 (ptm) cc_final: 0.4420 (mmt) REVERT: F 420 GLN cc_start: 0.5859 (pp30) cc_final: 0.5610 (pt0) outliers start: 54 outliers final: 35 residues processed: 287 average time/residue: 1.1942 time to fit residues: 402.0290 Evaluate side-chains 272 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 249 PHE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 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 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 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 376 ASN 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 9 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG 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 374 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN 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 Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 36 optimal weight: 0.0570 chunk 206 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 247 ASN C 80 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.196608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.173139 restraints weight = 24454.759| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.95 r_work: 0.4404 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19494 Z= 0.160 Angle : 0.724 12.165 26472 Z= 0.359 Chirality : 0.048 0.220 2994 Planarity : 0.005 0.052 3399 Dihedral : 9.320 68.094 2820 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.93 % Allowed : 28.17 % Favored : 68.90 % 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: -1.09 (0.17), residues: 2415 helix: 0.10 (0.16), residues: 1122 sheet: -1.20 (0.26), residues: 366 loop : -1.41 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 102 HIS 0.006 0.001 HIS F 8 PHE 0.032 0.001 PHE A 191 TYR 0.033 0.002 TYR C 187 ARG 0.012 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 904) hydrogen bonds : angle 5.41583 ( 2682) covalent geometry : bond 0.00368 (19485) covalent geometry : angle 0.72431 (26472) Misc. bond : bond 0.00366 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14116.25 seconds wall clock time: 250 minutes 8.97 seconds (15008.97 seconds total)