Starting phenix.real_space_refine on Mon Jan 20 16:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.map" model { file = "/net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yal_39102/01_2025/8yal_39102.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 15 5.49 5 S 105 5.16 5 C 9738 2.51 5 N 2654 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15498 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3423 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3356 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3338 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3349 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 377 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 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: {'GTP': 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: 9.99, per 1000 atoms: 0.64 Number of scatterers: 15498 At special positions: 0 Unit cell: (113.42, 109.18, 120.84, 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 105 16.00 P 15 15.00 O 2986 8.00 N 2654 7.00 C 9738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 12 sheets defined 51.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.598A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.823A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 43' Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.934A pdb=" N PHE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.217A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.227A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.538A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.727A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.146A pdb=" N TYR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 295 through 301 Proline residue: B 298 - end of helix removed outlier: 3.515A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 301' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.551A pdb=" N VAL B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 401 removed outlier: 4.040A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.792A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 4.209A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 20 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.888A pdb=" N ALA C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 119 through 122 removed outlier: 3.633A pdb=" N GLN C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 122' Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.199A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 69 through 78 removed outlier: 3.809A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.615A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 107 through 125 removed outlier: 3.837A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.976A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.621A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.705A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.563A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.723A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.099A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 425 removed outlier: 4.130A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'E' and resid 82 through 85 removed outlier: 4.664A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 85' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 128 removed outlier: 4.162A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.355A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.011A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.636A pdb=" N LEU E 227 " --> pdb=" O SER E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.914A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.847A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 384 through 400 removed outlier: 3.777A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.843A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.340A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 46 through 49 Processing helix chain 'F' and resid 69 through 78 removed outlier: 4.078A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 125 removed outlier: 4.268A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 180 through 195 removed outlier: 3.659A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 237 Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.811A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.234A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 425 removed outlier: 4.131A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 232 removed outlier: 4.306A pdb=" N ASP I 229 " --> pdb=" O ASP I 225 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 236 Processing helix chain 'I' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.888A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL B 66 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER B 140 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 165 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 200 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 271 through 272 removed outlier: 3.562A pdb=" N LEU B 318 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS B 352 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN B 356 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 319 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.839A pdb=" N SER C 82 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL C 77 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU C 84 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 75 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 86 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 72 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 3 removed outlier: 8.354A pdb=" N LYS C 85 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 117 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 87 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 115 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG C 89 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ALA C 146 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET C 110 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP C 148 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 112 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.061A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.061A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET D 164 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR D 166 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.821A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.852A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N VAL E 66 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU E 3 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU E 136 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N SER E 140 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE E 9 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN E 133 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 354 removed outlier: 8.421A pdb=" N LYS E 352 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL E 315 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY E 354 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU E 317 " --> pdb=" O GLY E 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.011A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS F 6 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 315 " --> pdb=" O LYS F 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 51 through 53 694 hydrogen bonds defined for protein. 2001 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: 5.32 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3262 1.33 - 1.45: 3902 1.45 - 1.58: 8500 1.58 - 1.70: 17 1.70 - 1.83: 175 Bond restraints: 15856 Sorted by residual: bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.579 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.582 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O5' G2P F 501 " pdb=" PA G2P F 501 " ideal model delta sigma weight residual 1.656 1.569 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" O5' G2P D 501 " pdb=" PA G2P D 501 " ideal model delta sigma weight residual 1.656 1.574 0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C3A G2P F 501 " pdb=" PB G2P F 501 " ideal model delta sigma weight residual 1.850 1.784 0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 15851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 21299 2.77 - 5.54: 205 5.54 - 8.31: 34 8.31 - 11.08: 11 11.08 - 13.85: 3 Bond angle restraints: 21552 Sorted by residual: angle pdb=" C3B ACO C 301 " pdb=" O3B ACO C 301 " pdb=" P3B ACO C 301 " ideal model delta sigma weight residual 121.12 111.15 9.97 1.00e+00 1.00e+00 9.94e+01 angle pdb=" P1A ACO C 301 " pdb=" O3A ACO C 301 " pdb=" P2A ACO C 301 " ideal model delta sigma weight residual 136.83 128.68 8.15 1.00e+00 1.00e+00 6.65e+01 angle pdb=" C GLN F 11 " pdb=" CA GLN F 11 " pdb=" CB GLN F 11 " ideal model delta sigma weight residual 110.90 101.11 9.79 1.58e+00 4.01e-01 3.84e+01 angle pdb=" N MET D 323 " pdb=" CA MET D 323 " pdb=" C MET D 323 " ideal model delta sigma weight residual 113.17 105.47 7.70 1.26e+00 6.30e-01 3.73e+01 angle pdb=" N LYS D 324 " pdb=" CA LYS D 324 " pdb=" C LYS D 324 " ideal model delta sigma weight residual 111.40 105.01 6.39 1.22e+00 6.72e-01 2.74e+01 ... (remaining 21547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 9174 32.01 - 64.01: 268 64.01 - 96.02: 27 96.02 - 128.03: 3 128.03 - 160.03: 6 Dihedral angle restraints: 9478 sinusoidal: 3813 harmonic: 5665 Sorted by residual: dihedral pdb=" C4' GTP E 501 " pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " ideal model delta sinusoidal sigma weight residual 260.87 100.84 160.03 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -50.38 154.97 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -49.92 154.51 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 9475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1897 0.054 - 0.108: 378 0.108 - 0.161: 73 0.161 - 0.215: 8 0.215 - 0.269: 2 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA ARG B 221 " pdb=" N ARG B 221 " pdb=" C ARG B 221 " pdb=" CB ARG B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLN F 11 " pdb=" N GLN F 11 " pdb=" C GLN F 11 " pdb=" CB GLN F 11 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' GTP E 501 " pdb=" C2' GTP E 501 " pdb=" C4' GTP E 501 " pdb=" O3' GTP E 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2355 not shown) Planarity restraints: 2797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO C 301 " 0.254 2.00e-02 2.50e+03 2.15e-01 5.79e+02 pdb=" C5P ACO C 301 " -0.058 2.00e-02 2.50e+03 pdb=" C6P ACO C 301 " 0.161 2.00e-02 2.50e+03 pdb=" N4P ACO C 301 " -0.371 2.00e-02 2.50e+03 pdb=" O5P ACO C 301 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C 301 " -0.088 2.00e-02 2.50e+03 7.30e-02 6.67e+01 pdb=" C9P ACO C 301 " 0.011 2.00e-02 2.50e+03 pdb=" CAP ACO C 301 " -0.062 2.00e-02 2.50e+03 pdb=" N8P ACO C 301 " 0.120 2.00e-02 2.50e+03 pdb=" O9P ACO C 301 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 321 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C MET D 321 " -0.055 2.00e-02 2.50e+03 pdb=" O MET D 321 " 0.021 2.00e-02 2.50e+03 pdb=" N SER D 322 " 0.018 2.00e-02 2.50e+03 ... (remaining 2794 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1862 2.75 - 3.29: 15556 3.29 - 3.82: 26904 3.82 - 4.36: 32662 4.36 - 4.90: 56709 Nonbonded interactions: 133693 Sorted by model distance: nonbonded pdb=" O LEU F 192 " pdb=" OG1 THR F 196 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP F 67 " pdb=" OG1 THR F 72 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN B 186 " pdb=" OH TYR B 408 " model vdw 2.237 3.040 nonbonded pdb=" O LEU D 273 " pdb=" NE2 GLN D 292 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASN D 184 " pdb=" OH TYR D 398 " model vdw 2.281 3.040 ... (remaining 133688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 36 or resid 48 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 366 or (r \ esid 367 and (name N or name CA or name C or name O or name CB )) or resid 368 t \ hrough 400 or (resid 401 through 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 through 439 or resid 501)) selection = (chain 'E' and (resid 1 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 439 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 1 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 427 or resid 501)) selection = (chain 'F' and (resid 1 through 173 or (resid 174 and (name N or name CA or name \ C or name O or name CB )) or resid 175 through 427 or resid 501)) } 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.004 0.137 15856 Z= 0.288 Angle : 0.680 13.853 21552 Z= 0.353 Chirality : 0.045 0.269 2358 Planarity : 0.006 0.215 2797 Dihedral : 15.427 160.033 5840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.12 % Allowed : 0.42 % Favored : 99.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1946 helix: 1.65 (0.18), residues: 809 sheet: -1.17 (0.31), residues: 270 loop : -0.52 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 21 HIS 0.003 0.001 HIS F 396 PHE 0.015 0.001 PHE C 157 TYR 0.017 0.001 TYR C 162 ARG 0.003 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ILE cc_start: 0.9384 (tp) cc_final: 0.9100 (tp) REVERT: C 57 MET cc_start: 0.8005 (mtp) cc_final: 0.7687 (mtm) REVERT: C 105 TYR cc_start: 0.8308 (m-80) cc_final: 0.8093 (m-80) REVERT: I 220 ASN cc_start: 0.8946 (t0) cc_final: 0.8075 (t0) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.3406 time to fit residues: 83.5507 Evaluate side-chains 130 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 0.0070 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS B 128 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 52 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 99 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.049079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.039886 restraints weight = 71388.323| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.73 r_work: 0.2837 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15856 Z= 0.224 Angle : 0.545 7.854 21552 Z= 0.279 Chirality : 0.043 0.178 2358 Planarity : 0.004 0.055 2797 Dihedral : 11.370 161.801 2273 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.48 % Allowed : 5.93 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1946 helix: 1.88 (0.19), residues: 809 sheet: -1.35 (0.28), residues: 309 loop : -0.24 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.007 0.001 HIS E 8 PHE 0.016 0.001 PHE C 147 TYR 0.011 0.001 TYR B 172 ARG 0.011 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.9022 (t70) cc_final: 0.8688 (p0) REVERT: C 53 ARG cc_start: 0.8197 (ptp90) cc_final: 0.7922 (ptp90) REVERT: C 85 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8194 (mmmt) REVERT: C 105 TYR cc_start: 0.8648 (m-80) cc_final: 0.8210 (m-80) REVERT: C 108 LYS cc_start: 0.9233 (tttm) cc_final: 0.8928 (tmtt) REVERT: C 114 ASP cc_start: 0.9111 (t0) cc_final: 0.8483 (m-30) REVERT: C 133 GLU cc_start: 0.9079 (tp30) cc_final: 0.8776 (tp30) REVERT: C 155 GLN cc_start: 0.9359 (mt0) cc_final: 0.9156 (mp10) REVERT: C 162 TYR cc_start: 0.7597 (m-80) cc_final: 0.7336 (m-80) REVERT: C 185 HIS cc_start: 0.8326 (p90) cc_final: 0.7920 (p90) REVERT: E 377 MET cc_start: 0.8888 (tmm) cc_final: 0.8619 (tmm) REVERT: I 219 ARG cc_start: 0.6855 (mmt-90) cc_final: 0.5938 (mmt-90) REVERT: I 220 ASN cc_start: 0.8347 (t0) cc_final: 0.7376 (t0) REVERT: I 224 HIS cc_start: 0.6181 (m170) cc_final: 0.5892 (m90) REVERT: I 231 MET cc_start: 0.8767 (mtm) cc_final: 0.8431 (ppp) REVERT: I 260 ARG cc_start: 0.9003 (ttm-80) cc_final: 0.8758 (tmt170) outliers start: 8 outliers final: 3 residues processed: 140 average time/residue: 0.3511 time to fit residues: 70.5520 Evaluate side-chains 128 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 0.0370 chunk 182 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 95 optimal weight: 0.0370 chunk 87 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040482 restraints weight = 71467.521| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.76 r_work: 0.2866 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15856 Z= 0.150 Angle : 0.506 7.758 21552 Z= 0.256 Chirality : 0.042 0.152 2358 Planarity : 0.004 0.059 2797 Dihedral : 11.201 160.342 2273 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.61 % Allowed : 8.35 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1946 helix: 1.97 (0.19), residues: 819 sheet: -1.34 (0.29), residues: 300 loop : -0.24 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 21 HIS 0.004 0.001 HIS E 8 PHE 0.012 0.001 PHE C 147 TYR 0.012 0.001 TYR C 92 ARG 0.006 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6497 (ttp) cc_final: 0.6288 (ttp) REVERT: B 271 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.8987 (p) REVERT: C 6 ASP cc_start: 0.9171 (t0) cc_final: 0.8548 (t0) REVERT: C 13 ASP cc_start: 0.8974 (t70) cc_final: 0.8648 (p0) REVERT: C 36 GLN cc_start: 0.9361 (tm-30) cc_final: 0.9145 (tm-30) REVERT: C 53 ARG cc_start: 0.8360 (ptp90) cc_final: 0.8065 (ptp90) REVERT: C 76 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8077 (tppt) REVERT: C 85 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8215 (mmmt) REVERT: C 89 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7343 (ttp80) REVERT: C 92 TYR cc_start: 0.9256 (m-80) cc_final: 0.9024 (m-80) REVERT: C 105 TYR cc_start: 0.8547 (m-80) cc_final: 0.7990 (m-80) REVERT: C 114 ASP cc_start: 0.9101 (t0) cc_final: 0.8446 (m-30) REVERT: C 126 ASN cc_start: 0.8908 (m-40) cc_final: 0.8469 (m110) REVERT: C 133 GLU cc_start: 0.9087 (tp30) cc_final: 0.8705 (tp30) REVERT: C 162 TYR cc_start: 0.7661 (m-80) cc_final: 0.7372 (m-80) REVERT: C 185 HIS cc_start: 0.8371 (p90) cc_final: 0.8014 (p90) REVERT: E 377 MET cc_start: 0.8935 (tmm) cc_final: 0.8324 (tmm) REVERT: F 406 MET cc_start: 0.9106 (tpp) cc_final: 0.8895 (tpp) REVERT: I 219 ARG cc_start: 0.6979 (mmt-90) cc_final: 0.6176 (mmt-90) REVERT: I 220 ASN cc_start: 0.7667 (t0) cc_final: 0.7374 (t0) REVERT: I 224 HIS cc_start: 0.6469 (m170) cc_final: 0.5953 (m90) outliers start: 10 outliers final: 2 residues processed: 137 average time/residue: 0.3320 time to fit residues: 65.8140 Evaluate side-chains 133 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 229 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038653 restraints weight = 73322.590| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.73 r_work: 0.2812 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15856 Z= 0.307 Angle : 0.562 7.999 21552 Z= 0.282 Chirality : 0.043 0.146 2358 Planarity : 0.004 0.059 2797 Dihedral : 11.068 160.075 2273 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.91 % Allowed : 8.78 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1946 helix: 2.04 (0.19), residues: 818 sheet: -1.22 (0.30), residues: 273 loop : -0.26 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 21 HIS 0.006 0.001 HIS E 8 PHE 0.011 0.001 PHE E 255 TYR 0.009 0.001 TYR B 161 ARG 0.008 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8672 (tmm) cc_final: 0.8141 (tmm) REVERT: C 6 ASP cc_start: 0.9091 (t0) cc_final: 0.8722 (t0) REVERT: C 13 ASP cc_start: 0.8964 (t70) cc_final: 0.8652 (p0) REVERT: C 26 TYR cc_start: 0.8811 (m-10) cc_final: 0.8597 (m-10) REVERT: C 53 ARG cc_start: 0.8457 (ptp90) cc_final: 0.8157 (ptp90) REVERT: C 85 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8151 (mmmt) REVERT: C 105 TYR cc_start: 0.8517 (m-80) cc_final: 0.7988 (m-80) REVERT: C 108 LYS cc_start: 0.9112 (tttm) cc_final: 0.8799 (tmtt) REVERT: C 114 ASP cc_start: 0.9137 (t0) cc_final: 0.8474 (m-30) REVERT: C 133 GLU cc_start: 0.9127 (tp30) cc_final: 0.8739 (tp30) REVERT: C 162 TYR cc_start: 0.7719 (m-80) cc_final: 0.7427 (m-80) REVERT: C 171 SER cc_start: 0.9401 (m) cc_final: 0.8866 (t) REVERT: C 185 HIS cc_start: 0.8500 (p90) cc_final: 0.7956 (p90) REVERT: D 257 MET cc_start: 0.9389 (mmp) cc_final: 0.9177 (mmm) REVERT: E 377 MET cc_start: 0.8993 (tmm) cc_final: 0.8210 (tmm) REVERT: F 406 MET cc_start: 0.9177 (tpp) cc_final: 0.8929 (tpp) REVERT: I 220 ASN cc_start: 0.7877 (t0) cc_final: 0.7474 (t0) REVERT: I 224 HIS cc_start: 0.6654 (m170) cc_final: 0.6146 (m90) REVERT: I 231 MET cc_start: 0.8683 (mtm) cc_final: 0.8395 (ppp) outliers start: 15 outliers final: 8 residues processed: 138 average time/residue: 0.3137 time to fit residues: 63.7036 Evaluate side-chains 135 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 229 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 40 optimal weight: 0.0020 chunk 113 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039992 restraints weight = 72366.161| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.88 r_work: 0.2842 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15856 Z= 0.144 Angle : 0.499 8.921 21552 Z= 0.249 Chirality : 0.042 0.148 2358 Planarity : 0.003 0.057 2797 Dihedral : 10.974 160.248 2273 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.79 % Allowed : 10.17 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1946 helix: 2.20 (0.19), residues: 815 sheet: -1.24 (0.29), residues: 286 loop : -0.18 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 21 HIS 0.002 0.000 HIS E 8 PHE 0.009 0.001 PHE C 115 TYR 0.009 0.001 TYR D 106 ARG 0.007 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8620 (tmm) cc_final: 0.7999 (tmm) REVERT: C 13 ASP cc_start: 0.9023 (t70) cc_final: 0.8673 (p0) REVERT: C 36 GLN cc_start: 0.9469 (tm-30) cc_final: 0.9218 (tm-30) REVERT: C 53 ARG cc_start: 0.8502 (ptp90) cc_final: 0.8191 (ptp90) REVERT: C 89 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7619 (ttp80) REVERT: C 105 TYR cc_start: 0.8517 (m-80) cc_final: 0.7947 (m-80) REVERT: C 108 LYS cc_start: 0.9238 (tttm) cc_final: 0.8896 (tmtt) REVERT: C 110 MET cc_start: 0.8851 (mmm) cc_final: 0.8513 (mmm) REVERT: C 114 ASP cc_start: 0.9142 (t0) cc_final: 0.8485 (m-30) REVERT: C 133 GLU cc_start: 0.9115 (tp30) cc_final: 0.8692 (tp30) REVERT: C 160 LYS cc_start: 0.9369 (tttm) cc_final: 0.9150 (ptmm) REVERT: C 162 TYR cc_start: 0.7741 (m-80) cc_final: 0.7467 (m-80) REVERT: C 171 SER cc_start: 0.9386 (m) cc_final: 0.8857 (t) REVERT: C 185 HIS cc_start: 0.8518 (p90) cc_final: 0.7951 (p90) REVERT: D 257 MET cc_start: 0.9310 (mmp) cc_final: 0.9084 (mmm) REVERT: E 377 MET cc_start: 0.9052 (tmm) cc_final: 0.8188 (tmm) REVERT: F 406 MET cc_start: 0.9218 (tpp) cc_final: 0.8921 (tpp) REVERT: I 220 ASN cc_start: 0.7797 (t0) cc_final: 0.7362 (t0) REVERT: I 224 HIS cc_start: 0.6747 (m170) cc_final: 0.6201 (m90) outliers start: 13 outliers final: 5 residues processed: 137 average time/residue: 0.3270 time to fit residues: 65.4745 Evaluate side-chains 132 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 35 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040087 restraints weight = 71766.279| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.87 r_work: 0.2852 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15856 Z= 0.152 Angle : 0.498 9.528 21552 Z= 0.248 Chirality : 0.042 0.146 2358 Planarity : 0.003 0.054 2797 Dihedral : 10.839 160.160 2273 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.54 % Allowed : 10.84 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1946 helix: 2.22 (0.19), residues: 816 sheet: -1.28 (0.29), residues: 308 loop : -0.03 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 21 HIS 0.003 0.001 HIS E 8 PHE 0.015 0.001 PHE E 255 TYR 0.008 0.001 TYR D 106 ARG 0.009 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8635 (tmm) cc_final: 0.7987 (tmm) REVERT: C 13 ASP cc_start: 0.9084 (t70) cc_final: 0.8765 (p0) REVERT: C 20 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7806 (ttm170) REVERT: C 36 GLN cc_start: 0.9460 (tm-30) cc_final: 0.9109 (tm-30) REVERT: C 53 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8188 (ptp90) REVERT: C 85 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8182 (mmmt) REVERT: C 89 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7729 (ttp80) REVERT: C 105 TYR cc_start: 0.8472 (m-80) cc_final: 0.7960 (m-80) REVERT: C 108 LYS cc_start: 0.9241 (tttm) cc_final: 0.8867 (tmtt) REVERT: C 114 ASP cc_start: 0.9117 (t0) cc_final: 0.8498 (m-30) REVERT: C 133 GLU cc_start: 0.9072 (tp30) cc_final: 0.8643 (tp30) REVERT: C 160 LYS cc_start: 0.9375 (tttm) cc_final: 0.9162 (ptmm) REVERT: C 171 SER cc_start: 0.9402 (m) cc_final: 0.8880 (t) REVERT: C 185 HIS cc_start: 0.8520 (p90) cc_final: 0.7905 (p90) REVERT: D 323 MET cc_start: 0.4666 (ptt) cc_final: 0.4250 (ttp) REVERT: E 377 MET cc_start: 0.9071 (tmm) cc_final: 0.8171 (tmm) REVERT: F 406 MET cc_start: 0.9267 (tpp) cc_final: 0.8978 (tpp) REVERT: I 220 ASN cc_start: 0.7772 (t0) cc_final: 0.7411 (t0) REVERT: I 224 HIS cc_start: 0.6807 (m170) cc_final: 0.6270 (m90) outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.3270 time to fit residues: 64.7649 Evaluate side-chains 134 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain I residue 217 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 36 optimal weight: 0.0770 chunk 133 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 64 optimal weight: 0.0670 overall best weight: 1.1078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.049093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.039747 restraints weight = 72665.875| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.87 r_work: 0.2839 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15856 Z= 0.185 Angle : 0.509 10.010 21552 Z= 0.254 Chirality : 0.042 0.145 2358 Planarity : 0.003 0.052 2797 Dihedral : 10.742 160.726 2273 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.67 % Allowed : 11.62 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1946 helix: 2.22 (0.19), residues: 822 sheet: -1.30 (0.29), residues: 308 loop : 0.01 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS E 8 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 92 ARG 0.005 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8660 (tmm) cc_final: 0.7930 (tmm) REVERT: C 13 ASP cc_start: 0.9087 (t70) cc_final: 0.8788 (p0) REVERT: C 20 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7999 (ttm170) REVERT: C 26 TYR cc_start: 0.8891 (m-10) cc_final: 0.8621 (m-10) REVERT: C 36 GLN cc_start: 0.9475 (tm-30) cc_final: 0.9124 (tm-30) REVERT: C 53 ARG cc_start: 0.8552 (ptp90) cc_final: 0.8228 (ptp90) REVERT: C 104 GLN cc_start: 0.9223 (mt0) cc_final: 0.9017 (mt0) REVERT: C 105 TYR cc_start: 0.8451 (m-80) cc_final: 0.7931 (m-80) REVERT: C 114 ASP cc_start: 0.9152 (t0) cc_final: 0.8533 (m-30) REVERT: C 133 GLU cc_start: 0.9080 (tp30) cc_final: 0.8610 (tp30) REVERT: C 160 LYS cc_start: 0.9362 (tttm) cc_final: 0.9131 (ptmm) REVERT: C 171 SER cc_start: 0.9401 (m) cc_final: 0.8872 (t) REVERT: C 185 HIS cc_start: 0.8563 (p90) cc_final: 0.7932 (p90) REVERT: D 300 MET cc_start: 0.8588 (mtt) cc_final: 0.8240 (mtt) REVERT: D 323 MET cc_start: 0.4584 (ptt) cc_final: 0.4142 (ttp) REVERT: E 377 MET cc_start: 0.9064 (tmm) cc_final: 0.8155 (tmm) REVERT: E 413 MET cc_start: 0.8992 (ttp) cc_final: 0.8457 (tmm) REVERT: F 406 MET cc_start: 0.9291 (tpp) cc_final: 0.8996 (tpp) REVERT: I 220 ASN cc_start: 0.7788 (t0) cc_final: 0.7370 (t0) REVERT: I 224 HIS cc_start: 0.6939 (m170) cc_final: 0.6388 (m90) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.3215 time to fit residues: 64.1510 Evaluate side-chains 133 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 190 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040229 restraints weight = 71962.520| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.83 r_work: 0.2860 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15856 Z= 0.154 Angle : 0.506 11.323 21552 Z= 0.250 Chirality : 0.042 0.146 2358 Planarity : 0.003 0.058 2797 Dihedral : 10.650 161.022 2273 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.67 % Allowed : 11.68 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1946 helix: 2.29 (0.19), residues: 815 sheet: -1.27 (0.29), residues: 308 loop : 0.04 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 21 HIS 0.003 0.000 HIS E 8 PHE 0.016 0.001 PHE E 255 TYR 0.008 0.001 TYR B 172 ARG 0.007 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8650 (tmm) cc_final: 0.7890 (tmm) REVERT: C 13 ASP cc_start: 0.9105 (t70) cc_final: 0.8787 (p0) REVERT: C 26 TYR cc_start: 0.8876 (m-10) cc_final: 0.8593 (m-10) REVERT: C 36 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9123 (tm-30) REVERT: C 53 ARG cc_start: 0.8543 (ptp90) cc_final: 0.8220 (ptp90) REVERT: C 85 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8231 (mmmt) REVERT: C 104 GLN cc_start: 0.9219 (mt0) cc_final: 0.9012 (mt0) REVERT: C 105 TYR cc_start: 0.8382 (m-80) cc_final: 0.7883 (m-80) REVERT: C 108 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8847 (tmtt) REVERT: C 114 ASP cc_start: 0.9111 (t0) cc_final: 0.8515 (m-30) REVERT: C 133 GLU cc_start: 0.9070 (tp30) cc_final: 0.8642 (tp30) REVERT: C 171 SER cc_start: 0.9400 (m) cc_final: 0.8881 (t) REVERT: C 185 HIS cc_start: 0.8575 (p90) cc_final: 0.7926 (p90) REVERT: D 257 MET cc_start: 0.9394 (mmp) cc_final: 0.9102 (mmm) REVERT: D 300 MET cc_start: 0.8476 (mtt) cc_final: 0.8137 (mtt) REVERT: D 323 MET cc_start: 0.4532 (ptt) cc_final: 0.4097 (ttp) REVERT: E 377 MET cc_start: 0.9075 (tmm) cc_final: 0.8083 (tmm) REVERT: F 406 MET cc_start: 0.9279 (tpp) cc_final: 0.8972 (tpp) REVERT: I 220 ASN cc_start: 0.7683 (t0) cc_final: 0.7320 (t0) REVERT: I 224 HIS cc_start: 0.6984 (m170) cc_final: 0.6471 (m90) REVERT: I 231 MET cc_start: 0.8093 (ppp) cc_final: 0.7831 (ppp) outliers start: 11 outliers final: 5 residues processed: 138 average time/residue: 0.3235 time to fit residues: 66.0116 Evaluate side-chains 132 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 6.9990 chunk 110 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.049211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039842 restraints weight = 72539.169| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.91 r_work: 0.2844 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15856 Z= 0.180 Angle : 0.518 11.258 21552 Z= 0.256 Chirality : 0.042 0.195 2358 Planarity : 0.003 0.051 2797 Dihedral : 10.550 161.578 2273 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.54 % Allowed : 11.62 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1946 helix: 2.32 (0.19), residues: 815 sheet: -1.26 (0.29), residues: 310 loop : 0.09 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.004 0.001 HIS E 8 PHE 0.010 0.001 PHE C 157 TYR 0.014 0.001 TYR C 161 ARG 0.008 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8635 (tmm) cc_final: 0.8030 (tmm) REVERT: C 13 ASP cc_start: 0.9114 (t70) cc_final: 0.8803 (p0) REVERT: C 26 TYR cc_start: 0.8853 (m-10) cc_final: 0.8460 (m-10) REVERT: C 36 GLN cc_start: 0.9454 (tm-30) cc_final: 0.9115 (tm-30) REVERT: C 53 ARG cc_start: 0.8595 (ptp90) cc_final: 0.8271 (ptp90) REVERT: C 85 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8111 (mmmt) REVERT: C 104 GLN cc_start: 0.9226 (mt0) cc_final: 0.9022 (mt0) REVERT: C 108 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8812 (tmtt) REVERT: C 110 MET cc_start: 0.8835 (mmm) cc_final: 0.8561 (mmm) REVERT: C 114 ASP cc_start: 0.9125 (t0) cc_final: 0.8509 (m-30) REVERT: C 133 GLU cc_start: 0.9069 (tp30) cc_final: 0.8641 (tp30) REVERT: C 171 SER cc_start: 0.9408 (m) cc_final: 0.8887 (t) REVERT: C 185 HIS cc_start: 0.8588 (p90) cc_final: 0.8188 (p90) REVERT: D 300 MET cc_start: 0.8548 (mtt) cc_final: 0.8284 (mtt) REVERT: D 323 MET cc_start: 0.4484 (ptt) cc_final: 0.4098 (ttp) REVERT: E 377 MET cc_start: 0.9081 (tmm) cc_final: 0.8089 (tmm) REVERT: E 413 MET cc_start: 0.8970 (ttp) cc_final: 0.8488 (tmm) REVERT: F 406 MET cc_start: 0.9299 (tpp) cc_final: 0.8994 (tpp) REVERT: I 220 ASN cc_start: 0.7740 (t0) cc_final: 0.7370 (t0) REVERT: I 224 HIS cc_start: 0.7011 (m170) cc_final: 0.6469 (m90) REVERT: I 231 MET cc_start: 0.8099 (ppp) cc_final: 0.7838 (ppp) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.3158 time to fit residues: 62.5452 Evaluate side-chains 133 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain I residue 217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 53 optimal weight: 0.0170 chunk 51 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039846 restraints weight = 72928.311| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.82 r_work: 0.2848 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15856 Z= 0.184 Angle : 0.536 12.750 21552 Z= 0.262 Chirality : 0.042 0.266 2358 Planarity : 0.003 0.050 2797 Dihedral : 10.485 161.961 2273 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.42 % Allowed : 11.86 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1946 helix: 2.31 (0.19), residues: 815 sheet: -1.30 (0.29), residues: 314 loop : 0.13 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS E 8 PHE 0.017 0.001 PHE E 255 TYR 0.008 0.001 TYR B 172 ARG 0.021 0.000 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.8652 (tmm) cc_final: 0.8035 (tmm) REVERT: C 13 ASP cc_start: 0.9113 (t70) cc_final: 0.8811 (p0) REVERT: C 26 TYR cc_start: 0.8834 (m-10) cc_final: 0.8429 (m-10) REVERT: C 36 GLN cc_start: 0.9449 (tm-30) cc_final: 0.9111 (tm-30) REVERT: C 53 ARG cc_start: 0.8593 (ptp90) cc_final: 0.8271 (ptp90) REVERT: C 92 TYR cc_start: 0.8913 (m-80) cc_final: 0.8526 (m-80) REVERT: C 104 GLN cc_start: 0.9217 (mt0) cc_final: 0.9008 (mt0) REVERT: C 108 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8749 (tmtt) REVERT: C 114 ASP cc_start: 0.9099 (t0) cc_final: 0.8473 (m-30) REVERT: C 126 ASN cc_start: 0.8728 (m-40) cc_final: 0.8404 (m-40) REVERT: C 133 GLU cc_start: 0.9045 (tp30) cc_final: 0.8623 (tp30) REVERT: C 162 TYR cc_start: 0.7798 (m-80) cc_final: 0.7539 (m-10) REVERT: C 171 SER cc_start: 0.9411 (m) cc_final: 0.8891 (t) REVERT: C 185 HIS cc_start: 0.8591 (p90) cc_final: 0.8180 (p90) REVERT: D 300 MET cc_start: 0.8583 (mtt) cc_final: 0.8364 (mtt) REVERT: D 323 MET cc_start: 0.4436 (ptt) cc_final: 0.4066 (ttp) REVERT: E 377 MET cc_start: 0.9061 (tmm) cc_final: 0.8089 (tmm) REVERT: E 413 MET cc_start: 0.8983 (ttp) cc_final: 0.8487 (tmm) REVERT: F 406 MET cc_start: 0.9304 (tpp) cc_final: 0.9002 (tpp) REVERT: I 220 ASN cc_start: 0.7748 (t0) cc_final: 0.7396 (t0) REVERT: I 224 HIS cc_start: 0.7029 (m170) cc_final: 0.6492 (m90) REVERT: I 231 MET cc_start: 0.8027 (ppp) cc_final: 0.7781 (ppp) outliers start: 7 outliers final: 6 residues processed: 133 average time/residue: 0.3085 time to fit residues: 61.7857 Evaluate side-chains 133 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain I residue 217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 83 optimal weight: 0.0070 chunk 180 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 144 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040151 restraints weight = 72452.807| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.89 r_work: 0.2856 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15856 Z= 0.153 Angle : 0.521 12.397 21552 Z= 0.255 Chirality : 0.042 0.255 2358 Planarity : 0.003 0.050 2797 Dihedral : 10.401 162.449 2273 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.48 % Allowed : 12.17 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1946 helix: 2.31 (0.19), residues: 815 sheet: -1.21 (0.29), residues: 310 loop : 0.07 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 21 HIS 0.003 0.000 HIS E 8 PHE 0.008 0.001 PHE D 167 TYR 0.013 0.001 TYR C 92 ARG 0.008 0.000 ARG I 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6682.44 seconds wall clock time: 122 minutes 3.29 seconds (7323.29 seconds total)