Starting phenix.real_space_refine on Mon Nov 18 04:53:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yaj_39100/11_2024/8yaj_39100.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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 12 5.49 5 S 107 5.16 5 C 9738 2.51 5 N 2646 2.21 5 O 2980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15483 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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': 20} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3360 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain: "E" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3345 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" 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: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 371 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PIN': 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: 10.07, per 1000 atoms: 0.65 Number of scatterers: 15483 At special positions: 0 Unit cell: (113.42, 110.24, 121.9, 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 107 16.00 P 12 15.00 O 2980 8.00 N 2646 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: 3.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 17 sheets defined 53.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.549A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.685A pdb=" N ASP B 47 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 48 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.528A pdb=" N SER B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.052A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.353A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.607A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 223 through 240 removed outlier: 3.780A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.051A pdb=" N HIS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.550A pdb=" N CYS B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 removed outlier: 3.618A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.541A pdb=" N HIS B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.508A pdb=" N VAL B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.837A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 removed outlier: 4.083A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 19 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.952A 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 99 through 103 removed outlier: 3.606A pdb=" N GLN C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 removed outlier: 4.473A pdb=" N ARG C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 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 45 removed outlier: 3.832A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.930A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 3.914A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.685A 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 106 Processing helix chain 'D' and resid 107 through 127 removed outlier: 4.109A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.568A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.328A 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: 3.719A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 4.048A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 373 through 391 removed outlier: 3.868A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.092A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 425 removed outlier: 3.760A 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 47 through 51 removed outlier: 3.885A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 81 through 86 removed outlier: 4.401A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) 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: 4.022A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.524A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.816A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 195 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 226 through 240 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: 3.795A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.934A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.707A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.755A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.929A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 437 removed outlier: 4.198A 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 40 through 44 Processing helix chain 'F' and resid 46 through 49 Processing helix chain 'F' and resid 69 through 78 removed outlier: 4.508A 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 107 through 126 removed outlier: 3.748A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 4.048A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.675A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.877A 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 removed outlier: 3.555A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 removed outlier: 3.513A pdb=" N ARG F 241 " --> pdb=" O THR F 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 295 Processing helix chain 'F' and resid 296 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 removed outlier: 3.713A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.939A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.097A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 425 removed outlier: 3.583A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.584A 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 226 through 231 Processing helix chain 'I' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'B' and resid 93 through 94 removed outlier: 8.710A pdb=" N VAL B 66 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS B 200 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94 removed outlier: 8.710A pdb=" N VAL B 66 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.562A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 374 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3 removed outlier: 5.788A pdb=" N LEU C 84 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 75 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY C 86 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET C 73 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 72 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 3 removed outlier: 7.355A pdb=" N GLY C 91 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE C 112 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 93 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N MET C 110 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 95 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS C 108 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ALA C 146 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET C 110 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.299A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.299A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET D 164 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 166 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'D' and resid 349 through 354 removed outlier: 4.049A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 92 through 94 removed outlier: 3.503A pdb=" N ASP E 69 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94 removed outlier: 3.503A pdb=" N ASP E 69 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 246 through 247 Processing sheet with id=AB7, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.135A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS F 6 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET F 164 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR F 166 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ALA F 352 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS F 354 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE F 317 " --> pdb=" O CYS F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 51 through 53 718 hydrogen bonds defined for protein. 2019 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: 5.21 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5097 1.34 - 1.48: 3982 1.48 - 1.62: 6575 1.62 - 1.77: 10 1.77 - 1.91: 176 Bond restraints: 15840 Sorted by residual: bond pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " ideal model delta sigma weight residual 1.610 1.833 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sigma weight residual 1.610 1.829 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C3A G2P D 501 " pdb=" PA G2P D 501 " ideal model delta sigma weight residual 1.818 1.656 0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C3A G2P F 501 " pdb=" PA G2P F 501 " ideal model delta sigma weight residual 1.818 1.658 0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " ideal model delta sigma weight residual 1.610 1.747 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 15835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 21290 2.72 - 5.45: 170 5.45 - 8.17: 41 8.17 - 10.90: 14 10.90 - 13.62: 8 Bond angle restraints: 21523 Sorted by residual: angle pdb=" O1A GTP E 501 " pdb=" PA GTP E 501 " pdb=" O5' GTP E 501 " ideal model delta sigma weight residual 108.20 94.58 13.62 3.00e+00 1.11e-01 2.06e+01 angle pdb=" O1A GTP B 501 " pdb=" PA GTP B 501 " pdb=" O5' GTP B 501 " ideal model delta sigma weight residual 108.20 94.88 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O2A GTP E 501 " pdb=" PA GTP E 501 " pdb=" O5' GTP E 501 " ideal model delta sigma weight residual 109.50 96.83 12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O2A GTP B 501 " pdb=" PA GTP B 501 " pdb=" O5' GTP B 501 " ideal model delta sigma weight residual 109.50 96.84 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O1A GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sigma weight residual 108.20 120.49 -12.29 3.00e+00 1.11e-01 1.68e+01 ... (remaining 21518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9260 35.92 - 71.83: 169 71.83 - 107.75: 17 107.75 - 143.66: 5 143.66 - 179.58: 5 Dihedral angle restraints: 9456 sinusoidal: 3782 harmonic: 5674 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -111.15 -179.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -95.66 164.93 1 2.00e+01 2.50e-03 4.72e+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 -58.45 163.04 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 9453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1944 0.057 - 0.113: 364 0.113 - 0.170: 33 0.170 - 0.226: 9 0.226 - 0.283: 6 Chirality restraints: 2356 Sorted by residual: 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 -2.76 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' GTP B 501 " pdb=" C2' GTP B 501 " pdb=" C4' GTP B 501 " pdb=" O3' GTP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C2' GTP E 501 " pdb=" C1' GTP E 501 " pdb=" C3' GTP E 501 " pdb=" O2' GTP E 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2353 not shown) Planarity restraints: 2794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 108 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C TYR E 108 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR E 108 " 0.014 2.00e-02 2.50e+03 pdb=" N THR E 109 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 388 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.01e+00 pdb=" CG TRP B 388 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 388 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 388 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 388 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 388 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 388 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 388 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 356 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 357 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.026 5.00e-02 4.00e+02 ... (remaining 2791 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1766 2.75 - 3.29: 15577 3.29 - 3.82: 26608 3.82 - 4.36: 31782 4.36 - 4.90: 55742 Nonbonded interactions: 131475 Sorted by model distance: nonbonded pdb=" OD1 ASN B 186 " pdb=" OH TYR B 408 " model vdw 2.209 3.040 nonbonded pdb=" NE2 GLN F 279 " pdb=" O ARG I 232 " model vdw 2.242 3.120 nonbonded pdb=" OE2 GLU F 27 " pdb=" OG SER F 234 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASN F 52 " pdb=" NH1 ARG F 62 " model vdw 2.279 3.120 nonbonded pdb=" O LEU D 192 " pdb=" OG1 THR D 196 " model vdw 2.289 3.040 ... (remaining 131470 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 37 or resid 46 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 through 112 or (resi \ d 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thro \ ugh 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) o \ r resid 221 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 through 366 or (resid 367 and (name N or name CA or \ name C or name O or name CB )) or resid 368 through 400 or (resid 401 through 40 \ 3 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' } ncs_group { reference = (chain 'D' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 427 or resid 501)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 35.910 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 15840 Z= 0.367 Angle : 0.701 13.624 21523 Z= 0.310 Chirality : 0.046 0.283 2356 Planarity : 0.004 0.048 2794 Dihedral : 15.603 179.578 5812 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1949 helix: 1.65 (0.18), residues: 848 sheet: -0.42 (0.34), residues: 266 loop : -0.71 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 388 HIS 0.006 0.001 HIS E 8 PHE 0.013 0.001 PHE D 260 TYR 0.031 0.001 TYR D 425 ARG 0.007 0.000 ARG I 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: C 124 SER cc_start: 0.9244 (m) cc_final: 0.8874 (p) REVERT: C 130 MET cc_start: 0.9527 (ttm) cc_final: 0.9322 (ttm) REVERT: C 138 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8841 (mm-30) REVERT: C 155 GLN cc_start: 0.9218 (mm110) cc_final: 0.8968 (mp10) REVERT: D 257 MET cc_start: 0.8166 (mmm) cc_final: 0.7852 (mmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2559 time to fit residues: 61.1891 Evaluate side-chains 123 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS I 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15840 Z= 0.190 Angle : 0.535 8.191 21523 Z= 0.271 Chirality : 0.043 0.222 2356 Planarity : 0.004 0.038 2794 Dihedral : 12.345 178.011 2235 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.54 % Allowed : 4.71 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1949 helix: 1.73 (0.18), residues: 857 sheet: -0.39 (0.34), residues: 254 loop : -0.58 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 388 HIS 0.007 0.001 HIS E 8 PHE 0.013 0.001 PHE E 255 TYR 0.015 0.001 TYR D 425 ARG 0.003 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8227 (ttm-80) REVERT: C 61 ILE cc_start: 0.9650 (mt) cc_final: 0.9422 (mp) REVERT: C 124 SER cc_start: 0.9238 (m) cc_final: 0.8860 (p) REVERT: C 159 GLU cc_start: 0.8640 (pp20) cc_final: 0.8431 (pp20) REVERT: D 257 MET cc_start: 0.8268 (mmm) cc_final: 0.7844 (mmm) outliers start: 9 outliers final: 5 residues processed: 137 average time/residue: 0.2668 time to fit residues: 56.9106 Evaluate side-chains 127 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 174 optimal weight: 0.0000 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS C 36 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS ** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15840 Z= 0.240 Angle : 0.520 7.143 21523 Z= 0.262 Chirality : 0.042 0.202 2356 Planarity : 0.003 0.038 2794 Dihedral : 11.835 177.150 2235 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.60 % Allowed : 7.61 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1949 helix: 1.80 (0.18), residues: 860 sheet: -0.46 (0.33), residues: 262 loop : -0.51 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 388 HIS 0.006 0.001 HIS E 8 PHE 0.013 0.001 PHE E 255 TYR 0.015 0.001 TYR B 432 ARG 0.004 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 SER cc_start: 0.9248 (m) cc_final: 0.8859 (p) REVERT: C 155 GLN cc_start: 0.8930 (mt0) cc_final: 0.8602 (mt0) REVERT: D 257 MET cc_start: 0.8272 (mmm) cc_final: 0.7873 (mmm) REVERT: D 403 MET cc_start: 0.7739 (mmm) cc_final: 0.7499 (mmm) outliers start: 10 outliers final: 4 residues processed: 127 average time/residue: 0.2619 time to fit residues: 52.6798 Evaluate side-chains 122 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 0.0270 chunk 186 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15840 Z= 0.198 Angle : 0.508 8.135 21523 Z= 0.254 Chirality : 0.042 0.203 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.981 178.046 2235 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.79 % Allowed : 8.70 % Favored : 90.52 % 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: 0.76 (0.20), residues: 1949 helix: 1.82 (0.18), residues: 861 sheet: -0.68 (0.32), residues: 265 loop : -0.44 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 388 HIS 0.004 0.001 HIS E 8 PHE 0.013 0.001 PHE B 255 TYR 0.014 0.001 TYR B 432 ARG 0.005 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8352 (ttm-80) REVERT: C 59 ASP cc_start: 0.8491 (m-30) cc_final: 0.8195 (m-30) REVERT: C 114 ASP cc_start: 0.8752 (t0) cc_final: 0.8440 (t0) REVERT: C 124 SER cc_start: 0.9240 (m) cc_final: 0.8857 (p) REVERT: D 257 MET cc_start: 0.8288 (mmm) cc_final: 0.7954 (mmm) REVERT: F 299 MET cc_start: 0.8529 (mmp) cc_final: 0.8278 (mmp) outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 0.3029 time to fit residues: 63.0377 Evaluate side-chains 125 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 15840 Z= 0.363 Angle : 0.584 8.727 21523 Z= 0.291 Chirality : 0.043 0.202 2356 Planarity : 0.004 0.038 2794 Dihedral : 10.736 174.255 2235 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.97 % Allowed : 9.84 % Favored : 89.19 % 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: 1949 helix: 1.81 (0.18), residues: 861 sheet: -0.93 (0.32), residues: 278 loop : -0.37 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 388 HIS 0.010 0.001 HIS F 6 PHE 0.011 0.001 PHE E 255 TYR 0.021 0.001 TYR B 432 ARG 0.005 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8386 (ttm-80) REVERT: C 124 SER cc_start: 0.9249 (m) cc_final: 0.8859 (p) REVERT: D 257 MET cc_start: 0.8327 (mmm) cc_final: 0.7968 (mmt) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.2598 time to fit residues: 52.1712 Evaluate side-chains 121 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 155 optimal weight: 0.0470 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15840 Z= 0.154 Angle : 0.505 9.011 21523 Z= 0.251 Chirality : 0.042 0.204 2356 Planarity : 0.003 0.039 2794 Dihedral : 10.536 178.535 2235 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.79 % Allowed : 10.75 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1949 helix: 1.83 (0.18), residues: 861 sheet: -0.85 (0.32), residues: 276 loop : -0.36 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP B 388 HIS 0.008 0.001 HIS F 6 PHE 0.013 0.001 PHE B 255 TYR 0.012 0.001 TYR B 432 ARG 0.006 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8409 (ttm-80) REVERT: C 124 SER cc_start: 0.9241 (m) cc_final: 0.8852 (p) REVERT: C 159 GLU cc_start: 0.8735 (pp20) cc_final: 0.8486 (pp20) REVERT: D 257 MET cc_start: 0.8273 (mmm) cc_final: 0.7898 (mmt) outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 0.2583 time to fit residues: 53.3148 Evaluate side-chains 125 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15840 Z= 0.170 Angle : 0.511 11.260 21523 Z= 0.254 Chirality : 0.042 0.188 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.283 179.815 2235 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.97 % Allowed : 11.05 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1949 helix: 1.83 (0.18), residues: 861 sheet: -0.87 (0.31), residues: 277 loop : -0.32 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 388 HIS 0.011 0.001 HIS B 107 PHE 0.009 0.001 PHE E 255 TYR 0.025 0.001 TYR B 108 ARG 0.004 0.000 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8443 (ttm-80) REVERT: C 36 GLN cc_start: 0.9096 (tt0) cc_final: 0.8869 (tm-30) REVERT: C 72 ILE cc_start: 0.9304 (mm) cc_final: 0.9043 (tp) REVERT: C 124 SER cc_start: 0.9260 (m) cc_final: 0.8822 (p) REVERT: C 159 GLU cc_start: 0.8750 (pp20) cc_final: 0.8507 (pp20) REVERT: D 257 MET cc_start: 0.8230 (mmm) cc_final: 0.7877 (mmt) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.2597 time to fit residues: 55.6495 Evaluate side-chains 133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN C 156 GLN D 195 ASN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15840 Z= 0.291 Angle : 0.574 11.535 21523 Z= 0.283 Chirality : 0.043 0.186 2356 Planarity : 0.003 0.037 2794 Dihedral : 10.245 178.382 2235 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.97 % Allowed : 11.53 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1949 helix: 1.82 (0.18), residues: 860 sheet: -0.96 (0.32), residues: 262 loop : -0.32 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 388 HIS 0.005 0.001 HIS F 6 PHE 0.017 0.001 PHE B 255 TYR 0.018 0.001 TYR B 108 ARG 0.006 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8459 (ttm-80) REVERT: C 124 SER cc_start: 0.9223 (m) cc_final: 0.8807 (p) REVERT: C 159 GLU cc_start: 0.8806 (pp20) cc_final: 0.8575 (pp20) REVERT: D 257 MET cc_start: 0.8315 (mmm) cc_final: 0.8022 (mmt) REVERT: F 257 MET cc_start: 0.7764 (mmm) cc_final: 0.7540 (mtp) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.2588 time to fit residues: 53.9556 Evaluate side-chains 127 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15840 Z= 0.255 Angle : 0.566 11.549 21523 Z= 0.278 Chirality : 0.042 0.189 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.150 179.736 2235 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.85 % Allowed : 11.71 % Favored : 87.44 % 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: 0.76 (0.20), residues: 1949 helix: 1.80 (0.18), residues: 861 sheet: -0.99 (0.32), residues: 261 loop : -0.29 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP B 388 HIS 0.006 0.001 HIS F 6 PHE 0.010 0.001 PHE F 200 TYR 0.014 0.001 TYR B 108 ARG 0.005 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.859 Fit side-chains REVERT: C 20 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8521 (ttm-80) REVERT: C 59 ASP cc_start: 0.8567 (m-30) cc_final: 0.8271 (m-30) REVERT: C 114 ASP cc_start: 0.8925 (t0) cc_final: 0.8493 (t0) REVERT: C 124 SER cc_start: 0.9215 (m) cc_final: 0.8827 (p) REVERT: C 155 GLN cc_start: 0.8947 (mt0) cc_final: 0.8593 (mp10) REVERT: C 159 GLU cc_start: 0.8820 (pp20) cc_final: 0.8598 (pp20) REVERT: D 257 MET cc_start: 0.8294 (mmm) cc_final: 0.7987 (mmt) REVERT: E 432 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8041 (t80) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.2752 time to fit residues: 57.4299 Evaluate side-chains 130 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15840 Z= 0.210 Angle : 0.558 12.164 21523 Z= 0.273 Chirality : 0.042 0.220 2356 Planarity : 0.003 0.038 2794 Dihedral : 9.995 177.655 2235 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.91 % Allowed : 11.78 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1949 helix: 1.80 (0.18), residues: 861 sheet: -0.92 (0.32), residues: 269 loop : -0.30 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 388 HIS 0.006 0.001 HIS F 6 PHE 0.018 0.001 PHE B 255 TYR 0.016 0.001 TYR B 108 ARG 0.005 0.000 ARG C 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8519 (ttm-80) REVERT: C 114 ASP cc_start: 0.8937 (t0) cc_final: 0.8504 (t0) REVERT: C 124 SER cc_start: 0.9208 (m) cc_final: 0.8809 (p) REVERT: C 156 GLN cc_start: 0.9109 (pt0) cc_final: 0.8773 (pm20) REVERT: C 159 GLU cc_start: 0.8804 (pp20) cc_final: 0.8577 (pp20) REVERT: D 257 MET cc_start: 0.8279 (mmm) cc_final: 0.7949 (mmt) REVERT: E 432 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8059 (t80) outliers start: 15 outliers final: 12 residues processed: 132 average time/residue: 0.2600 time to fit residues: 54.1569 Evaluate side-chains 130 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 157 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 137 HIS I 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.045959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037394 restraints weight = 78471.609| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.20 r_work: 0.2819 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15840 Z= 0.157 Angle : 0.555 12.594 21523 Z= 0.270 Chirality : 0.042 0.183 2356 Planarity : 0.003 0.047 2794 Dihedral : 9.725 172.011 2235 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.66 % Allowed : 12.26 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1949 helix: 1.79 (0.18), residues: 861 sheet: -0.94 (0.31), residues: 277 loop : -0.27 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 388 HIS 0.006 0.001 HIS F 6 PHE 0.009 0.001 PHE E 418 TYR 0.018 0.001 TYR B 108 ARG 0.008 0.000 ARG I 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2886.53 seconds wall clock time: 54 minutes 14.99 seconds (3254.99 seconds total)