Starting phenix.real_space_refine on Thu Sep 18 08:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_39100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_39100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_39100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_39100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaj_39100/09_2025/8yaj_39100.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 2} 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: {'ARG:plan': 3, 'GLU:plan': 2, '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: {'ARG:plan': 2, 'GLU:plan': 1, '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: 3.86, per 1000 atoms: 0.25 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: 1.32 Conformation dependent library (CDL) restraints added in 746.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.55 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: 2.63 Time building geometry restraints manager: 1.73 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 \ 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 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: 5.980 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- 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= 0.275 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG I 219 TYR 0.031 0.001 TYR D 425 PHE 0.013 0.001 PHE D 260 TRP 0.035 0.001 TRP B 388 HIS 0.006 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00561 (15840) covalent geometry : angle 0.70085 (21523) hydrogen bonds : bond 0.16212 ( 699) hydrogen bonds : angle 5.89609 ( 2019) *********************** 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 : 0.604 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: 0.1184 time to fit residues: 28.2176 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS B 301 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.036462 restraints weight = 78122.184| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.25 r_work: 0.2772 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 15840 Z= 0.204 Angle : 0.569 8.272 21523 Z= 0.290 Chirality : 0.044 0.185 2356 Planarity : 0.004 0.038 2794 Dihedral : 12.373 176.516 2235 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.60 % Allowed : 5.01 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.20), residues: 1949 helix: 1.74 (0.18), residues: 857 sheet: -0.42 (0.34), residues: 254 loop : -0.60 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 62 TYR 0.017 0.001 TYR C 105 PHE 0.014 0.001 PHE E 255 TRP 0.031 0.001 TRP B 388 HIS 0.009 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00449 (15840) covalent geometry : angle 0.56901 (21523) hydrogen bonds : bond 0.04169 ( 699) hydrogen bonds : angle 4.71697 ( 2019) *********************** 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 141 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.9041 (mmm) cc_final: 0.8573 (mmm) REVERT: B 302 MET cc_start: 0.8797 (mtt) cc_final: 0.8561 (mtt) REVERT: B 388 TRP cc_start: 0.8511 (m-90) cc_final: 0.7991 (m-90) REVERT: C 20 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7495 (ttm-80) REVERT: C 44 MET cc_start: 0.9020 (mtm) cc_final: 0.8698 (mtm) REVERT: C 61 ILE cc_start: 0.9082 (mt) cc_final: 0.8707 (mp) REVERT: C 73 MET cc_start: 0.8952 (ttp) cc_final: 0.8725 (ttm) REVERT: C 106 MET cc_start: 0.9080 (ttt) cc_final: 0.8715 (tpp) REVERT: C 124 SER cc_start: 0.9028 (m) cc_final: 0.8745 (p) REVERT: C 155 GLN cc_start: 0.9271 (mm110) cc_final: 0.8998 (mt0) REVERT: D 257 MET cc_start: 0.9098 (mmm) cc_final: 0.7923 (mmm) REVERT: D 403 MET cc_start: 0.8935 (tpp) cc_final: 0.8369 (mmm) REVERT: E 377 MET cc_start: 0.9100 (tmm) cc_final: 0.8849 (tmm) REVERT: F 321 MET cc_start: 0.9142 (ptp) cc_final: 0.8889 (ptp) outliers start: 10 outliers final: 4 residues processed: 135 average time/residue: 0.1141 time to fit residues: 24.0117 Evaluate side-chains 124 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 LEU 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 101 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 158 optimal weight: 0.0010 chunk 181 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN E 107 HIS ** I 224 HIS ** 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 = 0.3237 r_free = 0.3237 target = 0.046272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037452 restraints weight = 77317.908| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.26 r_work: 0.2810 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15840 Z= 0.104 Angle : 0.497 8.827 21523 Z= 0.252 Chirality : 0.042 0.177 2356 Planarity : 0.003 0.038 2794 Dihedral : 11.913 178.767 2235 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.72 % Allowed : 7.55 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.20), residues: 1949 helix: 1.75 (0.18), residues: 860 sheet: -0.52 (0.32), residues: 272 loop : -0.50 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 260 TYR 0.011 0.001 TYR B 432 PHE 0.013 0.001 PHE E 255 TRP 0.017 0.001 TRP B 388 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00229 (15840) covalent geometry : angle 0.49744 (21523) hydrogen bonds : bond 0.03593 ( 699) hydrogen bonds : angle 4.40650 ( 2019) *********************** 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 138 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 302 MET cc_start: 0.8731 (mtt) cc_final: 0.8431 (mtt) REVERT: B 377 MET cc_start: 0.9017 (tmm) cc_final: 0.8615 (tmm) REVERT: B 388 TRP cc_start: 0.8443 (m-90) cc_final: 0.7758 (m-90) REVERT: C 36 GLN cc_start: 0.9395 (tt0) cc_final: 0.9091 (tm-30) REVERT: C 44 MET cc_start: 0.9043 (mtm) cc_final: 0.8753 (mtm) REVERT: C 58 TYR cc_start: 0.7854 (t80) cc_final: 0.7644 (t80) REVERT: C 106 MET cc_start: 0.9119 (ttt) cc_final: 0.8823 (tpp) REVERT: C 124 SER cc_start: 0.9025 (m) cc_final: 0.8747 (p) REVERT: C 138 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9087 (mm-30) REVERT: C 159 GLU cc_start: 0.9453 (pp20) cc_final: 0.9228 (pp20) REVERT: C 185 HIS cc_start: 0.8525 (m90) cc_final: 0.8009 (m90) REVERT: D 257 MET cc_start: 0.9061 (mmm) cc_final: 0.7951 (mmm) REVERT: D 403 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8495 (mmm) REVERT: E 377 MET cc_start: 0.9092 (tmm) cc_final: 0.8758 (tmm) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.1141 time to fit residues: 23.5527 Evaluate side-chains 126 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 403 MET 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 137 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS I 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035863 restraints weight = 78527.677| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.14 r_work: 0.2752 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 15840 Z= 0.220 Angle : 0.556 7.915 21523 Z= 0.280 Chirality : 0.043 0.150 2356 Planarity : 0.004 0.038 2794 Dihedral : 11.126 175.421 2235 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.85 % Allowed : 9.48 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1949 helix: 1.82 (0.18), residues: 861 sheet: -0.87 (0.32), residues: 278 loop : -0.37 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 260 TYR 0.022 0.001 TYR B 432 PHE 0.012 0.001 PHE E 255 TRP 0.010 0.001 TRP E 21 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00480 (15840) covalent geometry : angle 0.55614 (21523) hydrogen bonds : bond 0.03747 ( 699) hydrogen bonds : angle 4.39478 ( 2019) *********************** 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 132 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9003 (tmm) cc_final: 0.8710 (tmm) REVERT: B 388 TRP cc_start: 0.8694 (m-90) cc_final: 0.8005 (m-90) REVERT: C 20 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7672 (ttm-80) REVERT: C 36 GLN cc_start: 0.9381 (tt0) cc_final: 0.9123 (tm-30) REVERT: C 44 MET cc_start: 0.9069 (mtm) cc_final: 0.8468 (mtt) REVERT: C 106 MET cc_start: 0.9087 (ttt) cc_final: 0.8840 (tpp) REVERT: C 114 ASP cc_start: 0.8796 (t0) cc_final: 0.8441 (t0) REVERT: C 124 SER cc_start: 0.8974 (m) cc_final: 0.8711 (p) REVERT: C 138 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9124 (mm-30) REVERT: C 185 HIS cc_start: 0.8573 (m90) cc_final: 0.8056 (m90) REVERT: D 257 MET cc_start: 0.9056 (mmm) cc_final: 0.7977 (mmt) REVERT: D 403 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8445 (mmm) REVERT: E 377 MET cc_start: 0.9088 (tmm) cc_final: 0.8653 (tmm) REVERT: E 413 MET cc_start: 0.9246 (tmm) cc_final: 0.8906 (tmm) REVERT: F 321 MET cc_start: 0.9191 (ptp) cc_final: 0.8951 (ptp) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 0.1097 time to fit residues: 22.1461 Evaluate side-chains 123 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 199 THR Chi-restraints excluded: chain D residue 403 MET 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 56 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 138 optimal weight: 0.0010 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** 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 = 0.3212 r_free = 0.3212 target = 0.045336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036669 restraints weight = 77435.925| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.20 r_work: 0.2776 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15840 Z= 0.131 Angle : 0.502 9.294 21523 Z= 0.253 Chirality : 0.042 0.159 2356 Planarity : 0.003 0.037 2794 Dihedral : 10.779 177.785 2235 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.79 % Allowed : 10.21 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1949 helix: 1.85 (0.18), residues: 861 sheet: -0.86 (0.31), residues: 286 loop : -0.35 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 260 TYR 0.015 0.001 TYR B 432 PHE 0.011 0.001 PHE E 255 TRP 0.010 0.001 TRP B 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00290 (15840) covalent geometry : angle 0.50210 (21523) hydrogen bonds : bond 0.03486 ( 699) hydrogen bonds : angle 4.27643 ( 2019) *********************** 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 134 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9035 (tmm) cc_final: 0.8691 (tmm) REVERT: B 388 TRP cc_start: 0.8699 (m-90) cc_final: 0.7934 (m-90) REVERT: C 20 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7677 (ttm-80) REVERT: C 36 GLN cc_start: 0.9382 (tt0) cc_final: 0.9137 (tm-30) REVERT: C 44 MET cc_start: 0.9092 (mtm) cc_final: 0.8760 (mtm) REVERT: C 106 MET cc_start: 0.9085 (ttt) cc_final: 0.8867 (tpp) REVERT: C 114 ASP cc_start: 0.8799 (t0) cc_final: 0.8413 (t0) REVERT: C 124 SER cc_start: 0.8978 (m) cc_final: 0.8714 (p) REVERT: C 138 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9097 (mm-30) REVERT: C 185 HIS cc_start: 0.8596 (m90) cc_final: 0.8053 (m90) REVERT: D 257 MET cc_start: 0.9065 (mmm) cc_final: 0.7943 (mmt) REVERT: D 403 MET cc_start: 0.8849 (tpp) cc_final: 0.8394 (mmm) REVERT: E 377 MET cc_start: 0.9082 (tmm) cc_final: 0.8620 (tmm) REVERT: F 6 HIS cc_start: 0.8921 (t70) cc_final: 0.8635 (t-170) REVERT: F 321 MET cc_start: 0.9230 (ptp) cc_final: 0.8939 (ptp) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.1110 time to fit residues: 22.7406 Evaluate side-chains 125 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 413 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 D residue 232 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 187 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 11 optimal weight: 0.0070 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036737 restraints weight = 77778.604| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.21 r_work: 0.2781 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15840 Z= 0.125 Angle : 0.496 7.551 21523 Z= 0.249 Chirality : 0.042 0.147 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.541 179.197 2235 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.15 % Allowed : 10.51 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.20), residues: 1949 helix: 1.88 (0.18), residues: 861 sheet: -0.85 (0.31), residues: 286 loop : -0.29 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 260 TYR 0.021 0.001 TYR B 108 PHE 0.014 0.001 PHE B 255 TRP 0.010 0.001 TRP E 21 HIS 0.007 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00280 (15840) covalent geometry : angle 0.49590 (21523) hydrogen bonds : bond 0.03385 ( 699) hydrogen bonds : angle 4.21087 ( 2019) *********************** 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 139 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9039 (tmm) cc_final: 0.8671 (tmm) REVERT: B 388 TRP cc_start: 0.8785 (m-90) cc_final: 0.7989 (m-90) REVERT: C 20 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7778 (ttm-80) REVERT: C 44 MET cc_start: 0.9119 (mtm) cc_final: 0.8768 (mtm) REVERT: C 106 MET cc_start: 0.9089 (ttt) cc_final: 0.8884 (tpp) REVERT: C 114 ASP cc_start: 0.8873 (t0) cc_final: 0.8455 (t0) REVERT: C 124 SER cc_start: 0.9003 (m) cc_final: 0.8728 (p) REVERT: C 138 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9079 (mm-30) REVERT: C 185 HIS cc_start: 0.8593 (m90) cc_final: 0.8074 (m90) REVERT: D 257 MET cc_start: 0.9023 (mmm) cc_final: 0.7919 (mmt) REVERT: D 403 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: E 377 MET cc_start: 0.9122 (tmm) cc_final: 0.8638 (tmm) REVERT: F 6 HIS cc_start: 0.8922 (t70) cc_final: 0.8651 (t-170) REVERT: F 233 MET cc_start: 0.9081 (mmm) cc_final: 0.8804 (mmm) REVERT: F 321 MET cc_start: 0.9196 (ptp) cc_final: 0.8870 (ptp) REVERT: F 323 MET cc_start: 0.8900 (mmm) cc_final: 0.8575 (mtm) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.1157 time to fit residues: 24.3501 Evaluate side-chains 129 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 232 THR Chi-restraints excluded: chain D residue 403 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 139 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 0.0370 chunk 169 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** 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 = 0.3225 r_free = 0.3225 target = 0.045588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036989 restraints weight = 77287.231| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.20 r_work: 0.2798 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1742 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= 0.115 Angle : 0.509 10.016 21523 Z= 0.253 Chirality : 0.042 0.134 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.276 178.679 2235 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.91 % Allowed : 11.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1949 helix: 1.89 (0.18), residues: 861 sheet: -0.89 (0.31), residues: 287 loop : -0.27 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 260 TYR 0.016 0.001 TYR B 108 PHE 0.009 0.001 PHE E 255 TRP 0.009 0.001 TRP E 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00259 (15840) covalent geometry : angle 0.50929 (21523) hydrogen bonds : bond 0.03291 ( 699) hydrogen bonds : angle 4.15110 ( 2019) *********************** 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 138 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9047 (tmm) cc_final: 0.8654 (tmm) REVERT: B 388 TRP cc_start: 0.8810 (m-90) cc_final: 0.8004 (m-90) REVERT: C 20 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7462 (ttt-90) REVERT: C 44 MET cc_start: 0.9108 (mtm) cc_final: 0.8763 (mtm) REVERT: C 71 TYR cc_start: 0.8866 (m-80) cc_final: 0.8155 (m-80) REVERT: C 114 ASP cc_start: 0.8913 (t0) cc_final: 0.8363 (t0) REVERT: C 124 SER cc_start: 0.9000 (m) cc_final: 0.8730 (p) REVERT: C 138 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9109 (mm-30) REVERT: C 185 HIS cc_start: 0.8614 (m90) cc_final: 0.8125 (m90) REVERT: D 257 MET cc_start: 0.8977 (mmm) cc_final: 0.7943 (mmt) REVERT: D 403 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: E 302 MET cc_start: 0.9420 (mtt) cc_final: 0.9175 (mmt) REVERT: E 377 MET cc_start: 0.9155 (tmm) cc_final: 0.8698 (tmm) REVERT: F 6 HIS cc_start: 0.8899 (t70) cc_final: 0.8628 (t-170) REVERT: F 323 MET cc_start: 0.8908 (mmm) cc_final: 0.8545 (mtm) outliers start: 15 outliers final: 12 residues processed: 134 average time/residue: 0.1168 time to fit residues: 24.5620 Evaluate side-chains 133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 D residue 403 MET 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 87 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** 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 = 0.3231 r_free = 0.3231 target = 0.045734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036871 restraints weight = 79112.753| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.29 r_work: 0.2800 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15840 Z= 0.109 Angle : 0.516 11.563 21523 Z= 0.253 Chirality : 0.041 0.138 2356 Planarity : 0.003 0.038 2794 Dihedral : 10.082 176.599 2235 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.91 % Allowed : 11.90 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1949 helix: 1.91 (0.18), residues: 865 sheet: -0.84 (0.31), residues: 277 loop : -0.27 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 260 TYR 0.012 0.001 TYR B 432 PHE 0.015 0.001 PHE B 255 TRP 0.009 0.001 TRP E 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00247 (15840) covalent geometry : angle 0.51617 (21523) hydrogen bonds : bond 0.03233 ( 699) hydrogen bonds : angle 4.10324 ( 2019) *********************** 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 140 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9022 (tmm) cc_final: 0.8630 (tmm) REVERT: B 388 TRP cc_start: 0.8832 (m-90) cc_final: 0.8036 (m-90) REVERT: C 20 ARG cc_start: 0.8359 (ttp80) cc_final: 0.7753 (ttm-80) REVERT: C 44 MET cc_start: 0.9103 (mtm) cc_final: 0.8755 (mtm) REVERT: C 66 GLU cc_start: 0.8703 (pm20) cc_final: 0.8497 (pm20) REVERT: C 71 TYR cc_start: 0.8878 (m-80) cc_final: 0.8158 (m-80) REVERT: C 114 ASP cc_start: 0.8929 (t0) cc_final: 0.8377 (t0) REVERT: C 124 SER cc_start: 0.8989 (m) cc_final: 0.8625 (p) REVERT: C 138 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9089 (mm-30) REVERT: C 185 HIS cc_start: 0.8571 (m90) cc_final: 0.8066 (m90) REVERT: D 257 MET cc_start: 0.8983 (mmm) cc_final: 0.7989 (mmt) REVERT: D 403 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8342 (mmm) REVERT: E 302 MET cc_start: 0.9409 (mtt) cc_final: 0.9195 (mmt) REVERT: E 377 MET cc_start: 0.9169 (tmm) cc_final: 0.8733 (tmm) REVERT: F 6 HIS cc_start: 0.8918 (t70) cc_final: 0.8663 (t-170) REVERT: F 164 MET cc_start: 0.8607 (mmm) cc_final: 0.8391 (mmm) REVERT: F 233 MET cc_start: 0.9099 (mmm) cc_final: 0.8847 (mmm) REVERT: F 300 MET cc_start: 0.8579 (mtt) cc_final: 0.8360 (mtt) REVERT: F 323 MET cc_start: 0.8952 (mmm) cc_final: 0.8554 (mtm) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.1065 time to fit residues: 23.3374 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 : 0.588 ------------------------------------------------------------------------------- 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 D residue 403 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 151 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 29 optimal weight: 0.0470 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036893 restraints weight = 78928.484| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.22 r_work: 0.2805 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15840 Z= 0.124 Angle : 0.529 12.087 21523 Z= 0.259 Chirality : 0.042 0.138 2356 Planarity : 0.003 0.038 2794 Dihedral : 9.928 174.900 2235 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.97 % Allowed : 12.26 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 1949 helix: 1.91 (0.18), residues: 865 sheet: -0.84 (0.31), residues: 277 loop : -0.24 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 260 TYR 0.013 0.001 TYR B 108 PHE 0.009 0.001 PHE E 255 TRP 0.009 0.001 TRP E 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00280 (15840) covalent geometry : angle 0.52944 (21523) hydrogen bonds : bond 0.03233 ( 699) hydrogen bonds : angle 4.10219 ( 2019) *********************** 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 140 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9044 (tmm) cc_final: 0.8638 (tmm) REVERT: B 388 TRP cc_start: 0.8862 (m-90) cc_final: 0.7983 (m-90) REVERT: C 20 ARG cc_start: 0.8433 (ttp80) cc_final: 0.7548 (ttt-90) REVERT: C 44 MET cc_start: 0.9108 (mtm) cc_final: 0.8742 (mtm) REVERT: C 114 ASP cc_start: 0.8960 (t0) cc_final: 0.8448 (t0) REVERT: C 124 SER cc_start: 0.8913 (m) cc_final: 0.8633 (p) REVERT: C 138 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9094 (mm-30) REVERT: C 185 HIS cc_start: 0.8594 (m90) cc_final: 0.8080 (m90) REVERT: D 257 MET cc_start: 0.8968 (mmm) cc_final: 0.7943 (mmt) REVERT: D 403 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8355 (mmm) REVERT: E 302 MET cc_start: 0.9420 (mtt) cc_final: 0.9185 (mmt) REVERT: E 377 MET cc_start: 0.9198 (tmm) cc_final: 0.8713 (tmm) REVERT: E 432 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8338 (t80) REVERT: F 6 HIS cc_start: 0.8923 (t70) cc_final: 0.8636 (t-170) REVERT: F 164 MET cc_start: 0.8549 (mmm) cc_final: 0.8333 (mmm) REVERT: F 233 MET cc_start: 0.9129 (mmm) cc_final: 0.8879 (mmm) REVERT: F 300 MET cc_start: 0.8616 (mtt) cc_final: 0.8363 (mtt) REVERT: F 323 MET cc_start: 0.8959 (mmm) cc_final: 0.8562 (mtm) outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.1134 time to fit residues: 24.0586 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 : 0.621 ------------------------------------------------------------------------------- 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 232 THR Chi-restraints excluded: chain D residue 403 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 118 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 119 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** 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 = 0.3226 r_free = 0.3226 target = 0.045224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036697 restraints weight = 79541.015| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.23 r_work: 0.2796 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15840 Z= 0.136 Angle : 0.536 12.219 21523 Z= 0.261 Chirality : 0.042 0.137 2356 Planarity : 0.003 0.038 2794 Dihedral : 9.797 172.858 2235 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.85 % Allowed : 12.26 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1949 helix: 1.96 (0.18), residues: 861 sheet: -0.85 (0.31), residues: 277 loop : -0.23 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 62 TYR 0.013 0.001 TYR B 432 PHE 0.018 0.001 PHE B 255 TRP 0.009 0.001 TRP E 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00306 (15840) covalent geometry : angle 0.53647 (21523) hydrogen bonds : bond 0.03282 ( 699) hydrogen bonds : angle 4.09480 ( 2019) ********************** 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 138 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.9051 (tmm) cc_final: 0.8644 (tmm) REVERT: B 388 TRP cc_start: 0.8895 (m-90) cc_final: 0.7989 (m-90) REVERT: C 20 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7543 (ttt-90) REVERT: C 36 GLN cc_start: 0.9337 (tt0) cc_final: 0.9049 (tm-30) REVERT: C 44 MET cc_start: 0.9091 (mtm) cc_final: 0.8583 (mtm) REVERT: C 58 TYR cc_start: 0.8003 (t80) cc_final: 0.7746 (t80) REVERT: C 71 TYR cc_start: 0.8793 (m-80) cc_final: 0.8115 (m-80) REVERT: C 114 ASP cc_start: 0.8944 (t0) cc_final: 0.8430 (t0) REVERT: C 124 SER cc_start: 0.8874 (m) cc_final: 0.8597 (p) REVERT: C 138 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9137 (mm-30) REVERT: C 185 HIS cc_start: 0.8570 (m90) cc_final: 0.8075 (m90) REVERT: D 257 MET cc_start: 0.8971 (mmm) cc_final: 0.7956 (mmt) REVERT: D 403 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8388 (mmm) REVERT: E 302 MET cc_start: 0.9426 (mtt) cc_final: 0.9169 (mmt) REVERT: E 377 MET cc_start: 0.9201 (tmm) cc_final: 0.8719 (tmm) REVERT: E 432 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8303 (t80) REVERT: F 6 HIS cc_start: 0.8924 (t70) cc_final: 0.8634 (t-170) REVERT: F 164 MET cc_start: 0.8526 (mmm) cc_final: 0.8314 (mmm) REVERT: F 233 MET cc_start: 0.9121 (mmm) cc_final: 0.8869 (mmm) REVERT: F 300 MET cc_start: 0.8682 (mtt) cc_final: 0.8401 (mtt) REVERT: F 321 MET cc_start: 0.9254 (ptp) cc_final: 0.8799 (ptp) REVERT: F 323 MET cc_start: 0.8969 (mmm) cc_final: 0.8572 (mtm) outliers start: 14 outliers final: 11 residues processed: 133 average time/residue: 0.1127 time to fit residues: 23.5710 Evaluate side-chains 137 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 232 THR Chi-restraints excluded: chain D residue 403 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** 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 = 0.3232 r_free = 0.3232 target = 0.045424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.036917 restraints weight = 78734.232| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.18 r_work: 0.2806 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15840 Z= 0.121 Angle : 0.533 12.223 21523 Z= 0.259 Chirality : 0.042 0.133 2356 Planarity : 0.003 0.038 2794 Dihedral : 9.623 169.155 2235 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.91 % Allowed : 12.14 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1949 helix: 1.96 (0.18), residues: 861 sheet: -0.86 (0.31), residues: 277 loop : -0.23 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 260 TYR 0.012 0.001 TYR B 108 PHE 0.009 0.001 PHE E 255 TRP 0.008 0.001 TRP E 21 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00275 (15840) covalent geometry : angle 0.53256 (21523) hydrogen bonds : bond 0.03199 ( 699) hydrogen bonds : angle 4.07095 ( 2019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.46 seconds wall clock time: 61 minutes 3.39 seconds (3663.39 seconds total)