Starting phenix.real_space_refine on Mon May 19 13:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.map" model { file = "/net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e26_47439/05_2025/9e26_47439.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.044 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 11374 2.51 5 N 3422 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18444 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.13, per 1000 atoms: 0.66 Number of scatterers: 18444 At special positions: 0 Unit cell: (129.78, 145.23, 94.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 10 15.00 Mg 4 11.99 O 3532 8.00 N 3422 7.00 C 11374 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: 5.45 Conformation dependent library (CDL) restraints added in 2.8 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 45.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.593A pdb=" N LEU A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 126 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.246A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.771A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.554A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 106 through 126 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.493A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 4.015A pdb=" N VAL B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.979A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 399 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.581A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 150 through 157 removed outlier: 4.315A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.592A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.617A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.625A pdb=" N LEU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.249A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.799A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.522A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.611A pdb=" N LEU E 105 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.162A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.968A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.859A pdb=" N GLY F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 150 through 157 removed outlier: 4.351A pdb=" N LEU F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.893A pdb=" N LYS F 247 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 4.112A pdb=" N LEU F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.615A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.879A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.743A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 278 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA A 423 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 280 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ARG A 425 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N ARG A 432 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU A 456 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.649A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.371A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 380 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 379 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 420 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 436 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.618A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.618A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 182 removed outlier: 4.641A pdb=" N VAL D 171 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 172 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE D 163 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 174 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.733A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 380 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N ARG D 432 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N GLU D 456 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.589A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 170 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 165 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE E 172 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE E 163 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU E 174 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.376A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 380 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 420 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE E 436 " --> pdb=" O ILE E 420 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN E 422 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 17.116A pdb=" N ARG E 431 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N THR E 458 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ILE E 433 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU E 456 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS E 435 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL E 454 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 437 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU E 452 " --> pdb=" O THR E 437 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL E 439 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN E 450 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.627A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.659A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY F 356 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS F 307 " --> pdb=" O GLY F 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU F 357 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS F 382 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU F 442 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2937 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: 6.40 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6552 1.34 - 1.46: 3189 1.46 - 1.58: 8757 1.58 - 1.70: 10 1.70 - 1.81: 168 Bond restraints: 18676 Sorted by residual: bond pdb=" C VAL E 145 " pdb=" N LEU E 146 " ideal model delta sigma weight residual 1.332 1.357 -0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" C VAL F 145 " pdb=" N LEU F 146 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.42e-02 4.96e+03 2.96e+00 bond pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.29e-02 6.01e+03 2.05e+00 bond pdb=" C4 ADP E 602 " pdb=" C5 ADP E 602 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 18671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24995 1.68 - 3.36: 259 3.36 - 5.04: 92 5.04 - 6.71: 19 6.71 - 8.39: 5 Bond angle restraints: 25370 Sorted by residual: angle pdb=" CG ARG F 491 " pdb=" CD ARG F 491 " pdb=" NE ARG F 491 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.94e+00 angle pdb=" CB MET A 399 " pdb=" CG MET A 399 " pdb=" SD MET A 399 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C3' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" C5' ATP A 602 " ideal model delta sigma weight residual 115.19 110.40 4.79 1.76e+00 3.23e-01 7.41e+00 angle pdb=" C2' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O3' ATP A 602 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" CB ARG C 491 " pdb=" CG ARG C 491 " pdb=" CD ARG C 491 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 ... (remaining 25365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 10387 17.46 - 34.92: 813 34.92 - 52.39: 207 52.39 - 69.85: 54 69.85 - 87.31: 23 Dihedral angle restraints: 11484 sinusoidal: 4284 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS D 435 " pdb=" C HIS D 435 " pdb=" N ILE D 436 " pdb=" CA ILE D 436 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS A 435 " pdb=" C HIS A 435 " pdb=" N ILE A 436 " pdb=" CA ILE A 436 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 11481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2523 0.060 - 0.120: 452 0.120 - 0.179: 29 0.179 - 0.239: 0 0.239 - 0.299: 6 Chirality restraints: 3010 Sorted by residual: chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' ATP D 602 " pdb=" C1' ATP D 602 " pdb=" C3' ATP D 602 " pdb=" O2' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP A 602 " pdb=" C1' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O2' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3007 not shown) Planarity restraints: 3364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 145 " -0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C VAL E 145 " 0.081 2.00e-02 2.50e+03 pdb=" O VAL E 145 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU E 146 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 145 " 0.024 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C VAL F 145 " -0.080 2.00e-02 2.50e+03 pdb=" O VAL F 145 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU F 146 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 491 " -0.255 9.50e-02 1.11e+02 1.15e-01 9.01e+00 pdb=" NE ARG C 491 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 491 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 491 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 491 " -0.003 2.00e-02 2.50e+03 ... (remaining 3361 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 146 2.49 - 3.09: 14455 3.09 - 3.69: 28311 3.69 - 4.30: 41231 4.30 - 4.90: 70423 Nonbonded interactions: 154566 Sorted by model distance: nonbonded pdb=" OG1 THR A 288 " pdb="MG MG A 601 " model vdw 1.886 2.170 nonbonded pdb=" OG1 THR D 288 " pdb="MG MG D 601 " model vdw 1.915 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ATP D 602 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR E 288 " pdb="MG MG E 601 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR B 288 " pdb="MG MG B 602 " model vdw 1.945 2.170 ... (remaining 154561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 80 through 501) selection = (chain 'B' and resid 80 through 501) selection = chain 'C' selection = (chain 'D' and resid 80 through 501) selection = (chain 'E' and resid 80 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: 0.100 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.090 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.005 0.040 18676 Z= 0.210 Angle : 0.535 8.393 25370 Z= 0.269 Chirality : 0.046 0.299 3010 Planarity : 0.004 0.115 3364 Dihedral : 14.678 87.311 6840 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.07 % Allowed : 10.14 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2520 helix: 2.62 (0.16), residues: 1140 sheet: -0.61 (0.23), residues: 472 loop : 0.35 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 481 HIS 0.003 0.001 HIS E 382 PHE 0.005 0.001 PHE D 480 TYR 0.006 0.001 TYR D 487 ARG 0.017 0.000 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.11418 ( 1004) hydrogen bonds : angle 5.63490 ( 2937) covalent geometry : bond 0.00470 (18676) covalent geometry : angle 0.53466 (25370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 748 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.7801 (mt) cc_final: 0.7153 (mt) REVERT: A 324 GLU cc_start: 0.6499 (tt0) cc_final: 0.6273 (tp30) REVERT: A 414 VAL cc_start: 0.7811 (t) cc_final: 0.7299 (p) REVERT: A 465 LYS cc_start: 0.5440 (mmmm) cc_final: 0.5061 (mtpp) REVERT: B 225 ASN cc_start: 0.7239 (t0) cc_final: 0.7014 (t0) REVERT: B 250 MET cc_start: 0.7076 (tpp) cc_final: 0.6670 (tpt) REVERT: B 465 LYS cc_start: 0.6633 (mmtp) cc_final: 0.6347 (tmtt) REVERT: C 171 VAL cc_start: 0.7248 (t) cc_final: 0.7015 (t) REVERT: C 298 ILE cc_start: 0.6915 (mt) cc_final: 0.6679 (mt) REVERT: C 299 ASP cc_start: 0.7424 (t0) cc_final: 0.7125 (t70) REVERT: C 325 THR cc_start: 0.6104 (p) cc_final: 0.5729 (p) REVERT: D 247 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7940 (tttt) REVERT: D 279 ILE cc_start: 0.7829 (mm) cc_final: 0.7529 (mm) REVERT: D 324 GLU cc_start: 0.8283 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 351 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7035 (mp0) REVERT: E 173 ILE cc_start: 0.8067 (pt) cc_final: 0.7549 (pp) REVERT: E 178 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7542 (mmmt) REVERT: E 191 GLN cc_start: 0.9157 (tt0) cc_final: 0.8891 (tt0) REVERT: E 193 MET cc_start: 0.8552 (tpt) cc_final: 0.8221 (tpp) REVERT: E 277 LEU cc_start: 0.8110 (tp) cc_final: 0.7554 (mt) REVERT: E 324 GLU cc_start: 0.7317 (tp30) cc_final: 0.7090 (tp30) REVERT: E 345 CYS cc_start: 0.8456 (m) cc_final: 0.7851 (m) REVERT: E 395 SER cc_start: 0.7007 (m) cc_final: 0.6684 (p) REVERT: E 443 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6206 (mp0) REVERT: E 453 PHE cc_start: 0.6852 (t80) cc_final: 0.6560 (m-80) REVERT: F 244 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7246 (mptp) REVERT: F 289 THR cc_start: 0.8131 (m) cc_final: 0.7914 (p) REVERT: F 409 ILE cc_start: 0.5523 (mt) cc_final: 0.5316 (mt) outliers start: 19 outliers final: 6 residues processed: 761 average time/residue: 1.1622 time to fit residues: 997.4885 Evaluate side-chains 467 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 460 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 244 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 50.0000 chunk 191 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS B 166 ASN B 180 GLN B 202 GLN B 344 ASN C 166 ASN C 180 GLN C 225 ASN C 344 ASN C 382 HIS D 225 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 470 HIS ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 225 ASN E 344 ASN E 382 HIS E 450 GLN F 374 HIS F 435 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091696 restraints weight = 41561.103| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.24 r_work: 0.3158 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18676 Z= 0.193 Angle : 0.785 14.913 25370 Z= 0.391 Chirality : 0.050 0.213 3010 Planarity : 0.006 0.097 3364 Dihedral : 7.318 86.917 2859 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 8.39 % Allowed : 20.78 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2520 helix: 2.19 (0.16), residues: 1150 sheet: -0.61 (0.22), residues: 516 loop : 0.55 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 481 HIS 0.007 0.001 HIS A 382 PHE 0.020 0.002 PHE A 297 TYR 0.014 0.002 TYR B 148 ARG 0.018 0.001 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1004) hydrogen bonds : angle 4.38777 ( 2937) covalent geometry : bond 0.00442 (18676) covalent geometry : angle 0.78491 (25370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 538 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8317 (p90) cc_final: 0.7774 (p90) REVERT: A 250 MET cc_start: 0.5441 (pmm) cc_final: 0.4496 (mmm) REVERT: A 270 ILE cc_start: 0.8324 (mt) cc_final: 0.8021 (mt) REVERT: A 297 PHE cc_start: 0.6694 (m-10) cc_final: 0.6383 (m-80) REVERT: A 314 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 324 GLU cc_start: 0.7386 (tt0) cc_final: 0.6787 (mm-30) REVERT: A 358 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7316 (t) REVERT: B 309 ASP cc_start: 0.7966 (p0) cc_final: 0.7662 (p0) REVERT: B 344 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8333 (t0) REVERT: B 358 VAL cc_start: 0.8236 (t) cc_final: 0.8026 (m) REVERT: B 384 ASN cc_start: 0.8139 (m-40) cc_final: 0.7193 (m-40) REVERT: B 431 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5555 (mmt180) REVERT: C 309 ASP cc_start: 0.8289 (p0) cc_final: 0.7972 (p0) REVERT: C 358 VAL cc_start: 0.8433 (m) cc_final: 0.7842 (p) REVERT: C 498 ASP cc_start: 0.8845 (p0) cc_final: 0.8577 (p0) REVERT: D 164 MET cc_start: 0.8607 (ptp) cc_final: 0.8242 (ptt) REVERT: D 302 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7410 (tt0) REVERT: D 308 GLU cc_start: 0.7462 (tt0) cc_final: 0.7103 (pt0) REVERT: D 324 GLU cc_start: 0.8454 (tt0) cc_final: 0.8127 (tt0) REVERT: D 351 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7530 (mp0) REVERT: D 407 LYS cc_start: 0.8226 (mppt) cc_final: 0.7575 (mmmm) REVERT: D 465 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8228 (mmmm) REVERT: E 164 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7673 (mtp) REVERT: E 191 GLN cc_start: 0.9246 (tt0) cc_final: 0.8779 (tt0) REVERT: E 306 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8252 (p) REVERT: E 308 GLU cc_start: 0.6768 (mt-10) cc_final: 0.5994 (mp0) REVERT: E 324 GLU cc_start: 0.8097 (tp30) cc_final: 0.7378 (mm-30) REVERT: E 338 MET cc_start: 0.8123 (tpp) cc_final: 0.7642 (tpp) REVERT: E 341 LEU cc_start: 0.7750 (mt) cc_final: 0.7484 (mm) REVERT: E 344 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7395 (t0) REVERT: E 370 MET cc_start: 0.8571 (mtt) cc_final: 0.8344 (mtt) REVERT: E 443 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6890 (mp0) REVERT: F 180 GLN cc_start: 0.8772 (pt0) cc_final: 0.8521 (pm20) REVERT: F 213 ILE cc_start: 0.8656 (pp) cc_final: 0.8103 (mp) REVERT: F 245 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7341 (tmmm) REVERT: F 262 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7581 (pm20) REVERT: F 289 THR cc_start: 0.8517 (m) cc_final: 0.8161 (p) REVERT: F 293 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8544 (p) REVERT: F 388 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: F 421 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7711 (mm) REVERT: F 439 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6607 (m) REVERT: F 480 PHE cc_start: 0.8023 (p90) cc_final: 0.7447 (p90) outliers start: 149 outliers final: 45 residues processed: 612 average time/residue: 1.0773 time to fit residues: 751.6309 Evaluate side-chains 509 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 454 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 475 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 164 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 36 optimal weight: 0.0020 chunk 217 optimal weight: 30.0000 chunk 190 optimal weight: 8.9990 chunk 235 optimal weight: 0.4980 chunk 224 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 overall best weight: 4.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 344 ASN A 371 ASN A 374 HIS ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 344 ASN C 276 ASN C 368 GLN C 384 ASN D 180 GLN D 191 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN E 166 ASN E 314 GLN E 368 GLN F 252 ASN F 382 HIS F 435 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.108622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087250 restraints weight = 41151.194| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.26 r_work: 0.3058 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 18676 Z= 0.208 Angle : 0.750 11.429 25370 Z= 0.376 Chirality : 0.049 0.225 3010 Planarity : 0.006 0.055 3364 Dihedral : 7.022 84.294 2851 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 7.21 % Allowed : 25.51 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2520 helix: 1.93 (0.15), residues: 1154 sheet: -0.53 (0.21), residues: 554 loop : 0.37 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 481 HIS 0.005 0.001 HIS E 470 PHE 0.019 0.002 PHE E 453 TYR 0.030 0.002 TYR C 148 ARG 0.011 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1004) hydrogen bonds : angle 4.23943 ( 2937) covalent geometry : bond 0.00476 (18676) covalent geometry : angle 0.74957 (25370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 482 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8487 (pt0) cc_final: 0.8220 (pt0) REVERT: A 242 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (ttpt) REVERT: A 247 LYS cc_start: 0.7113 (pmmt) cc_final: 0.6353 (mppt) REVERT: A 250 MET cc_start: 0.6176 (pmm) cc_final: 0.5627 (tpt) REVERT: A 290 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8461 (tm) REVERT: A 314 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8097 (tm-30) REVERT: A 324 GLU cc_start: 0.8074 (tt0) cc_final: 0.7027 (tp30) REVERT: A 340 ASP cc_start: 0.9006 (t0) cc_final: 0.8404 (m-30) REVERT: A 378 MET cc_start: 0.8497 (ptp) cc_final: 0.8138 (mtt) REVERT: A 434 THR cc_start: 0.8140 (p) cc_final: 0.7931 (p) REVERT: A 482 ASP cc_start: 0.8901 (t0) cc_final: 0.8313 (p0) REVERT: B 185 ARG cc_start: 0.7798 (pmt-80) cc_final: 0.7391 (ptp90) REVERT: B 186 PHE cc_start: 0.8543 (m-10) cc_final: 0.7868 (m-10) REVERT: B 250 MET cc_start: 0.7953 (tpp) cc_final: 0.7728 (tpp) REVERT: B 357 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: B 393 ILE cc_start: 0.8264 (mm) cc_final: 0.7921 (mt) REVERT: B 456 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 241 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7673 (mpp80) REVERT: C 273 CYS cc_start: 0.8174 (m) cc_final: 0.7702 (p) REVERT: C 421 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7939 (mt) REVERT: C 447 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4201 (pt) REVERT: D 351 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8022 (mp0) REVERT: D 407 LYS cc_start: 0.8386 (mppt) cc_final: 0.7822 (mmmm) REVERT: D 457 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7195 (mt) REVERT: D 469 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8135 (ptmm) REVERT: E 186 PHE cc_start: 0.7899 (m-10) cc_final: 0.7546 (m-10) REVERT: E 191 GLN cc_start: 0.9252 (tt0) cc_final: 0.8776 (tt0) REVERT: E 199 ILE cc_start: 0.8579 (pp) cc_final: 0.8358 (pp) REVERT: E 292 ASN cc_start: 0.8078 (m-40) cc_final: 0.7868 (m110) REVERT: E 324 GLU cc_start: 0.8441 (tp30) cc_final: 0.7796 (mm-30) REVERT: E 338 MET cc_start: 0.8498 (tpp) cc_final: 0.8049 (tpp) REVERT: E 344 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8062 (t0) REVERT: E 492 GLU cc_start: 0.7807 (tp30) cc_final: 0.6848 (tp30) REVERT: E 495 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8270 (pt0) REVERT: F 289 THR cc_start: 0.8898 (m) cc_final: 0.8580 (p) REVERT: F 307 CYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8538 (m) REVERT: F 312 GLU cc_start: 0.7709 (pm20) cc_final: 0.7493 (pm20) REVERT: F 388 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: F 421 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8237 (mm) REVERT: F 447 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.6097 (mt) REVERT: F 470 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7367 (t-90) outliers start: 128 outliers final: 50 residues processed: 558 average time/residue: 1.1278 time to fit residues: 713.0553 Evaluate side-chains 466 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 403 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 0.0170 chunk 79 optimal weight: 6.9990 chunk 158 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 42 optimal weight: 110.0000 chunk 142 optimal weight: 0.2980 chunk 187 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 overall best weight: 3.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 384 ASN B 276 ASN B 344 ASN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN E 202 GLN E 225 ASN E 314 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN F 382 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074125 restraints weight = 41730.086| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.13 r_work: 0.3018 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18676 Z= 0.166 Angle : 0.717 11.291 25370 Z= 0.352 Chirality : 0.048 0.185 3010 Planarity : 0.005 0.058 3364 Dihedral : 6.727 89.709 2847 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.87 % Allowed : 27.42 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2520 helix: 1.90 (0.15), residues: 1154 sheet: -0.27 (0.22), residues: 532 loop : 0.22 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 481 HIS 0.003 0.001 HIS D 435 PHE 0.035 0.002 PHE D 243 TYR 0.021 0.001 TYR C 148 ARG 0.011 0.001 ARG C 427 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 1004) hydrogen bonds : angle 4.08955 ( 2937) covalent geometry : bond 0.00395 (18676) covalent geometry : angle 0.71680 (25370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 424 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8923 (pptt) cc_final: 0.8558 (pptt) REVERT: A 180 GLN cc_start: 0.8753 (pt0) cc_final: 0.8494 (pm20) REVERT: A 192 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7957 (tm) REVERT: A 227 ILE cc_start: 0.8977 (mm) cc_final: 0.8687 (mm) REVERT: A 250 MET cc_start: 0.6507 (pmm) cc_final: 0.6210 (tpt) REVERT: A 265 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7490 (mtp180) REVERT: A 314 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8209 (tm-30) REVERT: A 324 GLU cc_start: 0.8418 (tt0) cc_final: 0.7530 (tp30) REVERT: A 340 ASP cc_start: 0.8931 (t0) cc_final: 0.8396 (m-30) REVERT: A 378 MET cc_start: 0.8709 (ptp) cc_final: 0.8497 (mtt) REVERT: A 450 GLN cc_start: 0.7941 (pp30) cc_final: 0.7716 (pp30) REVERT: A 469 LYS cc_start: 0.8103 (tptp) cc_final: 0.7687 (ttpp) REVERT: A 482 ASP cc_start: 0.9071 (t0) cc_final: 0.8480 (p0) REVERT: B 180 GLN cc_start: 0.8657 (pp30) cc_final: 0.8313 (pp30) REVERT: B 185 ARG cc_start: 0.7913 (pmt-80) cc_final: 0.7634 (ptp-110) REVERT: B 186 PHE cc_start: 0.8708 (m-10) cc_final: 0.7930 (m-10) REVERT: B 241 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7889 (mtp-110) REVERT: B 250 MET cc_start: 0.8027 (tpp) cc_final: 0.7667 (tpp) REVERT: B 323 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 339 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.7830 (ttm-80) REVERT: B 342 VAL cc_start: 0.8379 (t) cc_final: 0.8155 (t) REVERT: B 357 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: B 365 ASP cc_start: 0.8494 (m-30) cc_final: 0.8153 (m-30) REVERT: B 370 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6636 (mmt) REVERT: B 402 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: B 456 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: B 473 THR cc_start: 0.8530 (m) cc_final: 0.8208 (p) REVERT: B 498 ASP cc_start: 0.7989 (p0) cc_final: 0.7590 (m-30) REVERT: C 174 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: C 178 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7643 (tmmt) REVERT: C 193 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8633 (mmt) REVERT: C 244 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8452 (mptt) REVERT: C 273 CYS cc_start: 0.8496 (m) cc_final: 0.7825 (p) REVERT: C 337 THR cc_start: 0.8678 (m) cc_final: 0.8322 (p) REVERT: D 211 SER cc_start: 0.8946 (t) cc_final: 0.8574 (p) REVERT: D 351 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8177 (mp0) REVERT: D 396 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: D 469 LYS cc_start: 0.8906 (ptmm) cc_final: 0.8342 (ptmm) REVERT: E 180 GLN cc_start: 0.8156 (pm20) cc_final: 0.7828 (pm20) REVERT: E 186 PHE cc_start: 0.8215 (m-10) cc_final: 0.7927 (m-10) REVERT: E 191 GLN cc_start: 0.9248 (tt0) cc_final: 0.8731 (tt0) REVERT: E 213 ILE cc_start: 0.9274 (pt) cc_final: 0.9022 (pp) REVERT: E 215 ASP cc_start: 0.8820 (p0) cc_final: 0.8477 (t0) REVERT: E 324 GLU cc_start: 0.8622 (tp30) cc_final: 0.8049 (mm-30) REVERT: E 338 MET cc_start: 0.8526 (tpp) cc_final: 0.8091 (ttm) REVERT: E 407 LYS cc_start: 0.7983 (ptmt) cc_final: 0.7738 (tttp) REVERT: E 443 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7689 (mm-30) REVERT: E 492 GLU cc_start: 0.7911 (tp30) cc_final: 0.7048 (tp30) REVERT: E 495 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8164 (pt0) REVERT: E 498 ASP cc_start: 0.8202 (t0) cc_final: 0.7777 (p0) REVERT: F 206 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.7823 (ptm-80) REVERT: F 242 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9018 (mtpt) REVERT: F 289 THR cc_start: 0.9085 (m) cc_final: 0.8781 (p) REVERT: F 340 ASP cc_start: 0.8665 (m-30) cc_final: 0.8419 (m-30) REVERT: F 388 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: F 470 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7695 (t-90) outliers start: 122 outliers final: 44 residues processed: 503 average time/residue: 1.1182 time to fit residues: 636.5207 Evaluate side-chains 417 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 246 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 314 GLN E 344 ASN E 450 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078023 restraints weight = 40823.910| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.18 r_work: 0.2921 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 18676 Z= 0.222 Angle : 0.768 10.202 25370 Z= 0.384 Chirality : 0.050 0.251 3010 Planarity : 0.006 0.074 3364 Dihedral : 6.629 89.834 2847 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 7.38 % Allowed : 26.86 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2520 helix: 1.72 (0.15), residues: 1148 sheet: -0.40 (0.22), residues: 538 loop : 0.04 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 481 HIS 0.006 0.001 HIS A 374 PHE 0.030 0.002 PHE A 243 TYR 0.020 0.002 TYR C 487 ARG 0.014 0.001 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 1004) hydrogen bonds : angle 4.22873 ( 2937) covalent geometry : bond 0.00519 (18676) covalent geometry : angle 0.76829 (25370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 384 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (tm) REVERT: A 246 ASP cc_start: 0.8486 (t0) cc_final: 0.7919 (p0) REVERT: A 324 GLU cc_start: 0.8862 (tt0) cc_final: 0.8209 (tt0) REVERT: A 340 ASP cc_start: 0.8980 (t0) cc_final: 0.8777 (m-30) REVERT: A 343 LYS cc_start: 0.9300 (ttpp) cc_final: 0.9093 (ttmt) REVERT: A 378 MET cc_start: 0.9030 (ptp) cc_final: 0.8821 (mtt) REVERT: A 391 SER cc_start: 0.9109 (m) cc_final: 0.8869 (p) REVERT: A 398 THR cc_start: 0.9229 (m) cc_final: 0.8944 (p) REVERT: A 411 GLU cc_start: 0.8655 (pp20) cc_final: 0.8390 (pp20) REVERT: A 463 HIS cc_start: 0.8445 (m90) cc_final: 0.8118 (m90) REVERT: A 482 ASP cc_start: 0.9249 (t0) cc_final: 0.8999 (p0) REVERT: B 162 ASP cc_start: 0.7706 (m-30) cc_final: 0.7016 (m-30) REVERT: B 174 GLU cc_start: 0.8372 (tt0) cc_final: 0.7932 (tt0) REVERT: B 180 GLN cc_start: 0.8914 (pp30) cc_final: 0.8650 (pp30) REVERT: B 339 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8367 (ttm-80) REVERT: B 418 ASP cc_start: 0.8625 (t0) cc_final: 0.8409 (t0) REVERT: B 456 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: C 174 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: C 178 LYS cc_start: 0.8488 (tmmt) cc_final: 0.8129 (tmmt) REVERT: C 273 CYS cc_start: 0.8888 (m) cc_final: 0.8016 (p) REVERT: C 279 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7541 (mt) REVERT: C 324 GLU cc_start: 0.8895 (tt0) cc_final: 0.8052 (mm-30) REVERT: C 337 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8979 (p) REVERT: C 407 LYS cc_start: 0.8942 (tppp) cc_final: 0.8225 (tppt) REVERT: C 411 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8674 (mp0) REVERT: C 448 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (t) REVERT: C 498 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8929 (p0) REVERT: D 174 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: D 202 GLN cc_start: 0.8787 (tt0) cc_final: 0.7850 (tm-30) REVERT: D 211 SER cc_start: 0.9034 (t) cc_final: 0.8832 (t) REVERT: D 344 ASN cc_start: 0.9066 (t0) cc_final: 0.8606 (t0) REVERT: D 351 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8644 (mm-30) REVERT: D 394 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8810 (tt0) REVERT: D 407 LYS cc_start: 0.8751 (mmmm) cc_final: 0.7877 (mmmm) REVERT: D 411 GLU cc_start: 0.8531 (mp0) cc_final: 0.8243 (mp0) REVERT: D 445 ASP cc_start: 0.8636 (p0) cc_final: 0.8208 (t70) REVERT: D 469 LYS cc_start: 0.9210 (ptmm) cc_final: 0.8762 (ptmm) REVERT: E 180 GLN cc_start: 0.8723 (pm20) cc_final: 0.8397 (pm20) REVERT: E 186 PHE cc_start: 0.8743 (m-10) cc_final: 0.8319 (m-80) REVERT: E 191 GLN cc_start: 0.9287 (tt0) cc_final: 0.8657 (tt0) REVERT: E 247 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7710 (mtpp) REVERT: E 251 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8565 (tppp) REVERT: E 324 GLU cc_start: 0.8844 (tp30) cc_final: 0.8365 (mm-30) REVERT: E 338 MET cc_start: 0.8924 (tpp) cc_final: 0.8660 (ttm) REVERT: E 344 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8460 (t0) REVERT: E 406 SER cc_start: 0.8625 (p) cc_final: 0.8410 (p) REVERT: E 407 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8329 (tttp) REVERT: E 445 ASP cc_start: 0.9014 (t0) cc_final: 0.8380 (t0) REVERT: E 495 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8377 (pt0) REVERT: E 498 ASP cc_start: 0.8441 (t0) cc_final: 0.8041 (p0) REVERT: F 197 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8761 (mt0) REVERT: F 242 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9172 (mtpt) REVERT: F 294 MET cc_start: 0.9399 (tpp) cc_final: 0.8787 (tpt) REVERT: F 388 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: F 470 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.7889 (t-90) outliers start: 131 outliers final: 35 residues processed: 475 average time/residue: 1.3493 time to fit residues: 713.2890 Evaluate side-chains 365 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 87 optimal weight: 50.0000 chunk 134 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 2 optimal weight: 50.0000 chunk 152 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 141 optimal weight: 0.0770 chunk 192 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 374 HIS C 382 HIS D 191 GLN D 368 GLN D 450 GLN E 202 GLN E 314 GLN E 344 ASN F 435 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080893 restraints weight = 41898.893| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.19 r_work: 0.2910 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.9159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18676 Z= 0.160 Angle : 0.695 10.858 25370 Z= 0.342 Chirality : 0.047 0.230 3010 Planarity : 0.005 0.056 3364 Dihedral : 6.412 83.449 2847 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.84 % Allowed : 30.52 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2520 helix: 1.90 (0.16), residues: 1156 sheet: -0.27 (0.22), residues: 516 loop : -0.01 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 481 HIS 0.005 0.001 HIS D 463 PHE 0.033 0.002 PHE D 243 TYR 0.022 0.002 TYR C 486 ARG 0.013 0.001 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1004) hydrogen bonds : angle 4.06275 ( 2937) covalent geometry : bond 0.00385 (18676) covalent geometry : angle 0.69510 (25370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 345 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8402 (tm) REVERT: A 246 ASP cc_start: 0.8441 (t0) cc_final: 0.7893 (p0) REVERT: A 312 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7710 (tt0) REVERT: A 324 GLU cc_start: 0.8811 (tt0) cc_final: 0.8133 (tt0) REVERT: A 343 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9040 (ttmt) REVERT: A 359 ARG cc_start: 0.9247 (ptp90) cc_final: 0.8903 (ptp90) REVERT: A 398 THR cc_start: 0.9298 (m) cc_final: 0.9006 (p) REVERT: A 411 GLU cc_start: 0.8459 (pp20) cc_final: 0.8203 (tp30) REVERT: A 463 HIS cc_start: 0.8537 (m90) cc_final: 0.8214 (m90) REVERT: A 482 ASP cc_start: 0.9279 (t0) cc_final: 0.9068 (p0) REVERT: B 162 ASP cc_start: 0.7749 (m-30) cc_final: 0.7508 (m-30) REVERT: B 180 GLN cc_start: 0.9008 (pp30) cc_final: 0.8580 (pp30) REVERT: B 205 ARG cc_start: 0.9107 (mtp-110) cc_final: 0.8896 (mtp-110) REVERT: B 339 ARG cc_start: 0.8824 (ttp-170) cc_final: 0.8571 (ttm-80) REVERT: B 402 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: B 456 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: C 174 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: C 178 LYS cc_start: 0.8595 (tmmt) cc_final: 0.8301 (tmmt) REVERT: C 202 GLN cc_start: 0.8889 (tt0) cc_final: 0.8612 (mt0) REVERT: C 244 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8566 (mptt) REVERT: C 273 CYS cc_start: 0.8859 (m) cc_final: 0.8007 (p) REVERT: C 279 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7705 (mt) REVERT: C 324 GLU cc_start: 0.8886 (tt0) cc_final: 0.7963 (mm-30) REVERT: C 337 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 343 LYS cc_start: 0.9326 (mtmm) cc_final: 0.9053 (mmtp) REVERT: C 407 LYS cc_start: 0.8977 (tppp) cc_final: 0.8264 (tppt) REVERT: C 411 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8683 (mp0) REVERT: C 498 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8886 (p0) REVERT: D 211 SER cc_start: 0.9035 (t) cc_final: 0.8703 (p) REVERT: D 247 LYS cc_start: 0.8770 (mppt) cc_final: 0.8548 (mmtm) REVERT: D 314 GLN cc_start: 0.8878 (pm20) cc_final: 0.8666 (pm20) REVERT: D 351 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8408 (mp0) REVERT: D 394 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8878 (tt0) REVERT: D 407 LYS cc_start: 0.8916 (mmmm) cc_final: 0.7939 (mmmm) REVERT: D 411 GLU cc_start: 0.8558 (mp0) cc_final: 0.8275 (mp0) REVERT: D 469 LYS cc_start: 0.9161 (ptmm) cc_final: 0.8710 (ptmm) REVERT: E 180 GLN cc_start: 0.8671 (pm20) cc_final: 0.8309 (pm20) REVERT: E 186 PHE cc_start: 0.8817 (m-80) cc_final: 0.8457 (m-80) REVERT: E 191 GLN cc_start: 0.9290 (tt0) cc_final: 0.8675 (tt0) REVERT: E 324 GLU cc_start: 0.8898 (tp30) cc_final: 0.8403 (mm-30) REVERT: E 338 MET cc_start: 0.8895 (tpp) cc_final: 0.8633 (ttm) REVERT: E 344 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8554 (t0) REVERT: E 406 SER cc_start: 0.8655 (p) cc_final: 0.8440 (p) REVERT: E 407 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8441 (tttp) REVERT: E 445 ASP cc_start: 0.9044 (t0) cc_final: 0.8461 (t0) REVERT: E 498 ASP cc_start: 0.8480 (t0) cc_final: 0.7983 (t0) REVERT: F 197 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: F 206 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7926 (ptm-80) REVERT: F 294 MET cc_start: 0.9401 (tpp) cc_final: 0.8873 (tpt) REVERT: F 351 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: F 388 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: F 469 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9084 (tmmm) REVERT: F 470 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7775 (t-90) outliers start: 86 outliers final: 30 residues processed: 403 average time/residue: 1.3521 time to fit residues: 606.0472 Evaluate side-chains 342 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 84 optimal weight: 120.0000 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 41 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN B 317 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 202 GLN E 314 GLN E 344 ASN F 225 ASN F 314 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082294 restraints weight = 41612.392| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.20 r_work: 0.2956 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.9300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18676 Z= 0.136 Angle : 0.691 13.095 25370 Z= 0.339 Chirality : 0.047 0.199 3010 Planarity : 0.005 0.075 3364 Dihedral : 6.299 82.265 2847 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.11 % Allowed : 30.97 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2520 helix: 2.05 (0.16), residues: 1142 sheet: -0.15 (0.22), residues: 516 loop : -0.13 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 481 HIS 0.002 0.000 HIS D 435 PHE 0.027 0.001 PHE F 256 TYR 0.023 0.002 TYR B 486 ARG 0.016 0.001 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 1004) hydrogen bonds : angle 3.96407 ( 2937) covalent geometry : bond 0.00327 (18676) covalent geometry : angle 0.69080 (25370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8384 (tm) REVERT: A 246 ASP cc_start: 0.8388 (t0) cc_final: 0.7905 (p0) REVERT: A 316 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8612 (pt0) REVERT: A 324 GLU cc_start: 0.8790 (tt0) cc_final: 0.8074 (tt0) REVERT: A 359 ARG cc_start: 0.9275 (ptp90) cc_final: 0.8967 (ptp90) REVERT: A 398 THR cc_start: 0.9291 (m) cc_final: 0.9005 (p) REVERT: A 411 GLU cc_start: 0.8420 (pp20) cc_final: 0.8209 (tp30) REVERT: A 463 HIS cc_start: 0.8545 (m90) cc_final: 0.8194 (m90) REVERT: A 482 ASP cc_start: 0.9302 (t0) cc_final: 0.9072 (p0) REVERT: B 180 GLN cc_start: 0.8981 (pp30) cc_final: 0.8594 (pp30) REVERT: B 197 GLN cc_start: 0.8243 (pt0) cc_final: 0.7867 (pt0) REVERT: B 244 LYS cc_start: 0.8593 (tppt) cc_final: 0.8254 (tttp) REVERT: B 339 ARG cc_start: 0.8814 (ttp-170) cc_final: 0.8457 (ttm-80) REVERT: B 343 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8864 (mttp) REVERT: B 456 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: C 174 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: C 178 LYS cc_start: 0.8675 (tmmt) cc_final: 0.8426 (tmmt) REVERT: C 202 GLN cc_start: 0.8853 (tt0) cc_final: 0.8560 (mt0) REVERT: C 273 CYS cc_start: 0.8869 (m) cc_final: 0.8020 (p) REVERT: C 279 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7692 (mt) REVERT: C 324 GLU cc_start: 0.8908 (tt0) cc_final: 0.7963 (mm-30) REVERT: C 339 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8398 (tpt-90) REVERT: C 407 LYS cc_start: 0.8955 (tppp) cc_final: 0.8194 (tppt) REVERT: C 411 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8643 (mp0) REVERT: C 465 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8483 (mtmm) REVERT: C 498 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8942 (p0) REVERT: D 174 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: D 190 LEU cc_start: 0.9140 (mm) cc_final: 0.8917 (tm) REVERT: D 202 GLN cc_start: 0.8689 (tt0) cc_final: 0.7834 (tm-30) REVERT: D 211 SER cc_start: 0.9086 (t) cc_final: 0.8750 (p) REVERT: D 314 GLN cc_start: 0.8898 (pm20) cc_final: 0.8515 (mp10) REVERT: D 351 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8395 (mp0) REVERT: D 407 LYS cc_start: 0.8931 (mmmm) cc_final: 0.7494 (mmmm) REVERT: D 411 GLU cc_start: 0.8562 (mp0) cc_final: 0.8218 (mp0) REVERT: D 450 GLN cc_start: 0.8521 (pt0) cc_final: 0.8316 (pt0) REVERT: D 469 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8707 (ptmm) REVERT: E 180 GLN cc_start: 0.8633 (pm20) cc_final: 0.8261 (pm20) REVERT: E 186 PHE cc_start: 0.8848 (m-80) cc_final: 0.8471 (m-80) REVERT: E 191 GLN cc_start: 0.9271 (tt0) cc_final: 0.8647 (tt0) REVERT: E 324 GLU cc_start: 0.8855 (tp30) cc_final: 0.8446 (mm-30) REVERT: E 344 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8513 (t0) REVERT: E 406 SER cc_start: 0.8651 (p) cc_final: 0.8432 (p) REVERT: E 407 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8396 (tttp) REVERT: E 445 ASP cc_start: 0.9043 (t0) cc_final: 0.8492 (t0) REVERT: E 498 ASP cc_start: 0.8508 (t0) cc_final: 0.8001 (t0) REVERT: F 206 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7934 (ptm-80) REVERT: F 312 GLU cc_start: 0.8077 (pm20) cc_final: 0.7798 (pm20) REVERT: F 351 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: F 388 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: F 418 ASP cc_start: 0.8837 (m-30) cc_final: 0.8534 (m-30) REVERT: F 470 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7870 (t-90) outliers start: 73 outliers final: 32 residues processed: 378 average time/residue: 1.3695 time to fit residues: 574.7933 Evaluate side-chains 340 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7528 > 50: distance: 19 - 40: 5.894 distance: 24 - 48: 11.208 distance: 28 - 55: 29.695 distance: 36 - 40: 4.164 distance: 37 - 61: 25.482 distance: 40 - 41: 6.089 distance: 41 - 42: 13.588 distance: 41 - 44: 6.828 distance: 42 - 43: 8.913 distance: 42 - 48: 20.117 distance: 44 - 45: 36.949 distance: 44 - 46: 30.813 distance: 48 - 49: 17.635 distance: 49 - 50: 14.128 distance: 49 - 52: 12.244 distance: 50 - 51: 13.826 distance: 50 - 55: 18.551 distance: 52 - 53: 22.414 distance: 52 - 54: 9.055 distance: 55 - 56: 10.944 distance: 56 - 57: 26.537 distance: 56 - 59: 4.596 distance: 57 - 58: 13.924 distance: 57 - 61: 24.203 distance: 59 - 60: 10.469 distance: 61 - 62: 22.973 distance: 62 - 63: 14.396 distance: 62 - 65: 26.257 distance: 63 - 64: 9.510 distance: 63 - 70: 16.471 distance: 65 - 66: 26.991 distance: 66 - 67: 19.205 distance: 67 - 68: 19.191 distance: 67 - 69: 9.832 distance: 70 - 71: 6.262 distance: 71 - 72: 12.116 distance: 71 - 74: 15.650 distance: 72 - 73: 7.673 distance: 72 - 77: 12.866 distance: 74 - 75: 28.882 distance: 74 - 76: 8.204 distance: 77 - 78: 5.805 distance: 78 - 79: 5.363 distance: 79 - 80: 15.739 distance: 79 - 81: 8.300 distance: 81 - 82: 11.758 distance: 82 - 83: 11.869 distance: 82 - 85: 6.362 distance: 83 - 84: 21.893 distance: 83 - 92: 24.068 distance: 85 - 86: 20.262 distance: 86 - 87: 21.564 distance: 87 - 88: 16.791 distance: 88 - 89: 8.733 distance: 89 - 90: 17.667 distance: 89 - 91: 13.586 distance: 92 - 93: 19.910 distance: 93 - 94: 7.196 distance: 93 - 96: 23.286 distance: 94 - 95: 3.561 distance: 96 - 97: 17.042 distance: 97 - 98: 10.966 distance: 98 - 99: 15.184 distance: 99 - 100: 11.083 distance: 100 - 101: 28.517 distance: 100 - 102: 15.540 distance: 103 - 104: 8.495 distance: 104 - 107: 14.124 distance: 105 - 106: 11.189 distance: 105 - 110: 6.945 distance: 107 - 109: 48.633 distance: 110 - 111: 20.558 distance: 111 - 112: 23.676 distance: 111 - 114: 28.153 distance: 112 - 113: 13.180 distance: 112 - 118: 8.317 distance: 114 - 115: 17.856 distance: 115 - 116: 23.471 distance: 115 - 117: 4.851