Starting phenix.real_space_refine on Sat Oct 11 22:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pn2_17768/10_2025/8pn2_17768.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 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 18 5.49 5 Mg 6 5.21 5 S 72 5.16 5 C 11676 2.51 5 N 3216 2.21 5 O 3510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "F" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 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: 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: "C" 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: "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: 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: "F" 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} Time building chain proxies: 4.18, per 1000 atoms: 0.23 Number of scatterers: 18498 At special positions: 0 Unit cell: (125.46, 124.64, 99.22, 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 72 16.00 P 18 15.00 Mg 6 11.99 O 3510 8.00 N 3216 7.00 C 11676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 813.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 24.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.625A pdb=" N TYR A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 446 through 460 removed outlier: 3.512A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 4.015A pdb=" N TYR B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 73 " --> pdb=" O TYR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.594A pdb=" N PHE B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 73 removed outlier: 3.707A pdb=" N TYR C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 446 through 459 removed outlier: 3.539A pdb=" N PHE C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 73 removed outlier: 3.702A pdb=" N TYR D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.538A pdb=" N PHE D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 73 removed outlier: 4.042A pdb=" N TYR E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 327 through 331 Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 446 through 459 removed outlier: 3.576A pdb=" N PHE E 459 " --> pdb=" O GLN E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 72 removed outlier: 3.562A pdb=" N TYR F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 186 through 194 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 327 through 331 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 432 through 440 Processing helix chain 'F' and resid 446 through 460 removed outlier: 3.513A pdb=" N PHE F 459 " --> pdb=" O GLN F 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.718A pdb=" N ARG D 265 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 3.611A pdb=" N GLY A 114 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE A 129 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 122 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 127 " --> pdb=" O ARG A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 136 current: chain 'A' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 172 current: chain 'A' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 286 through 288 current: chain 'A' and resid 345 through 358 removed outlier: 5.750A pdb=" N THR A 349 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY A 373 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 351 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 371 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 353 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 369 " --> pdb=" O TYR A 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 364 through 373 current: chain 'A' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 400 through 405 current: chain 'A' and resid 424 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443 removed outlier: 3.731A pdb=" N ARG A 265 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 247 removed outlier: 3.595A pdb=" N GLY A 261 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.792A pdb=" N ARG E 265 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 122 removed outlier: 3.589A pdb=" N GLY B 114 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 129 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ARG B 122 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR B 127 " --> pdb=" O ARG B 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 136 current: chain 'B' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 170 current: chain 'B' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 286 through 288 current: chain 'B' and resid 344 through 358 removed outlier: 5.794A pdb=" N THR B 349 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY B 373 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET B 351 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 371 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR B 353 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 369 " --> pdb=" O TYR B 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 373 current: chain 'B' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 400 through 405 current: chain 'B' and resid 424 through 431 Processing sheet with id=AA8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'B' and resid 441 through 443 removed outlier: 3.790A pdb=" N ARG B 265 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 247 removed outlier: 3.526A pdb=" N GLY B 261 " --> pdb=" O MET B 246 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.742A pdb=" N ARG F 265 " --> pdb=" O PHE F 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 122 removed outlier: 5.216A pdb=" N ILE C 129 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG C 122 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR C 127 " --> pdb=" O ARG C 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 136 current: chain 'C' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 170 current: chain 'C' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 288 current: chain 'C' and resid 344 through 358 removed outlier: 5.753A pdb=" N THR C 349 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY C 373 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET C 351 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 371 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 353 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 369 " --> pdb=" O TYR C 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 364 through 373 current: chain 'C' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 400 through 405 current: chain 'C' and resid 424 through 431 Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AB5, first strand: chain 'C' and resid 441 through 443 removed outlier: 3.728A pdb=" N ARG C 265 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 245 through 247 removed outlier: 3.561A pdb=" N GLY C 261 " --> pdb=" O MET C 246 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 122 removed outlier: 5.215A pdb=" N ILE D 129 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG D 122 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR D 127 " --> pdb=" O ARG D 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 136 current: chain 'D' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 172 current: chain 'D' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 286 through 288 current: chain 'D' and resid 345 through 358 removed outlier: 5.694A pdb=" N THR D 349 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY D 373 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET D 351 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 371 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR D 353 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 369 " --> pdb=" O TYR D 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 373 current: chain 'D' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 400 through 405 current: chain 'D' and resid 424 through 431 Processing sheet with id=AB8, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB9, first strand: chain 'D' and resid 245 through 247 removed outlier: 3.512A pdb=" N GLY D 261 " --> pdb=" O MET D 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 122 removed outlier: 3.588A pdb=" N GLY E 114 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE E 129 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ARG E 122 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR E 127 " --> pdb=" O ARG E 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 136 current: chain 'E' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 172 current: chain 'E' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 286 through 288 current: chain 'E' and resid 344 through 358 removed outlier: 5.748A pdb=" N THR E 349 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY E 373 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET E 351 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL E 371 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 353 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 369 " --> pdb=" O TYR E 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 364 through 373 current: chain 'E' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 400 through 405 current: chain 'E' and resid 424 through 431 Processing sheet with id=AC2, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AC3, first strand: chain 'E' and resid 245 through 247 Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 122 removed outlier: 3.563A pdb=" N GLY F 114 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE F 129 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ARG F 122 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N THR F 127 " --> pdb=" O ARG F 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 125 through 136 current: chain 'F' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 170 current: chain 'F' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 286 through 288 current: chain 'F' and resid 344 through 358 removed outlier: 5.732A pdb=" N THR F 349 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY F 373 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET F 351 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL F 371 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR F 353 " --> pdb=" O ILE F 369 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 369 " --> pdb=" O TYR F 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 364 through 373 current: chain 'F' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 400 through 405 current: chain 'F' and resid 424 through 431 Processing sheet with id=AC5, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AC6, first strand: chain 'F' and resid 245 through 247 removed outlier: 3.570A pdb=" N GLY F 261 " --> pdb=" O MET F 246 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1173 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: 3.21 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6167 1.34 - 1.46: 4311 1.46 - 1.58: 8296 1.58 - 1.70: 24 1.70 - 1.81: 96 Bond restraints: 18894 Sorted by residual: bond pdb=" CA ILE E 129 " pdb=" C ILE E 129 " ideal model delta sigma weight residual 1.524 1.511 0.013 8.30e-03 1.45e+04 2.52e+00 bond pdb=" N ASP F 128 " pdb=" CA ASP F 128 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.96e+00 bond pdb=" N ASP A 128 " pdb=" CA ASP A 128 " ideal model delta sigma weight residual 1.460 1.476 -0.016 1.54e-02 4.22e+03 1.14e+00 bond pdb=" CA ASP A 128 " pdb=" CB ASP A 128 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.08e+00 bond pdb=" CA ASP F 128 " pdb=" CB ASP F 128 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.36e-01 ... (remaining 18889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 25034 1.35 - 2.69: 483 2.69 - 4.04: 128 4.04 - 5.38: 15 5.38 - 6.73: 14 Bond angle restraints: 25674 Sorted by residual: angle pdb=" N GLY D 257 " pdb=" CA GLY D 257 " pdb=" C GLY D 257 " ideal model delta sigma weight residual 110.38 115.63 -5.25 1.48e+00 4.57e-01 1.26e+01 angle pdb=" N GLY E 194 " pdb=" CA GLY E 194 " pdb=" C GLY E 194 " ideal model delta sigma weight residual 113.18 119.91 -6.73 2.37e+00 1.78e-01 8.06e+00 angle pdb=" N GLY A 194 " pdb=" CA GLY A 194 " pdb=" C GLY A 194 " ideal model delta sigma weight residual 113.18 119.79 -6.61 2.37e+00 1.78e-01 7.78e+00 angle pdb=" N GLY C 194 " pdb=" CA GLY C 194 " pdb=" C GLY C 194 " ideal model delta sigma weight residual 113.18 119.79 -6.61 2.37e+00 1.78e-01 7.77e+00 angle pdb=" N GLY B 194 " pdb=" CA GLY B 194 " pdb=" C GLY B 194 " ideal model delta sigma weight residual 113.18 119.72 -6.54 2.37e+00 1.78e-01 7.62e+00 ... (remaining 25669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 10060 17.79 - 35.59: 871 35.59 - 53.38: 147 53.38 - 71.18: 77 71.18 - 88.97: 29 Dihedral angle restraints: 11184 sinusoidal: 4536 harmonic: 6648 Sorted by residual: dihedral pdb=" CA MET C 184 " pdb=" C MET C 184 " pdb=" N PHE C 185 " pdb=" CA PHE C 185 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP F 368 " pdb=" CB ASP F 368 " pdb=" CG ASP F 368 " pdb=" OD1 ASP F 368 " ideal model delta sinusoidal sigma weight residual -30.00 -88.69 58.69 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA MET A 184 " pdb=" C MET A 184 " pdb=" N PHE A 185 " pdb=" CA PHE A 185 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 11181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2121 0.040 - 0.079: 457 0.079 - 0.119: 240 0.119 - 0.159: 31 0.159 - 0.198: 7 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CG LEU D 239 " pdb=" CB LEU D 239 " pdb=" CD1 LEU D 239 " pdb=" CD2 LEU D 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU A 239 " pdb=" CB LEU A 239 " pdb=" CD1 LEU A 239 " pdb=" CD2 LEU A 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU E 239 " pdb=" CB LEU E 239 " pdb=" CD1 LEU E 239 " pdb=" CD2 LEU E 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 2853 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 144 " -0.016 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP E 144 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP E 144 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP E 144 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 144 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 144 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 146 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO F 147 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 147 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 147 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 127 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C THR A 127 " -0.024 2.00e-02 2.50e+03 pdb=" O THR A 127 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 128 " 0.008 2.00e-02 2.50e+03 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 266 2.55 - 3.14: 14334 3.14 - 3.73: 31010 3.73 - 4.31: 44876 4.31 - 4.90: 73220 Nonbonded interactions: 163706 Sorted by model distance: nonbonded pdb=" OD1 ASP A 166 " pdb="MG MG A1002 " model vdw 1.969 2.170 nonbonded pdb=" OD1 ASP F 166 " pdb="MG MG F1002 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASP B 166 " pdb="MG MG B1002 " model vdw 1.977 2.170 nonbonded pdb=" OD1 ASP E 166 " pdb="MG MG E1002 " model vdw 1.984 2.170 nonbonded pdb=" O ILE A 121 " pdb="MG MG A1002 " model vdw 1.984 2.170 ... (remaining 163701 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.003 0.036 18894 Z= 0.113 Angle : 0.515 6.728 25674 Z= 0.272 Chirality : 0.043 0.198 2856 Planarity : 0.003 0.039 3318 Dihedral : 15.375 88.972 6948 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.05 % Allowed : 1.58 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.17), residues: 2334 helix: -0.23 (0.26), residues: 402 sheet: -0.32 (0.21), residues: 510 loop : 0.12 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 341 TYR 0.020 0.001 TYR F 69 PHE 0.017 0.001 PHE E 111 TRP 0.027 0.002 TRP E 144 HIS 0.007 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00252 (18894) covalent geometry : angle 0.51548 (25674) hydrogen bonds : bond 0.21547 ( 447) hydrogen bonds : angle 7.88375 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7893 (m-80) cc_final: 0.7585 (m-80) REVERT: A 184 MET cc_start: 0.7034 (ppp) cc_final: 0.6707 (ppp) REVERT: A 416 LYS cc_start: 0.8276 (tptm) cc_final: 0.7211 (mptt) REVERT: A 438 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7324 (tpp-160) REVERT: B 197 GLU cc_start: 0.7641 (pt0) cc_final: 0.7134 (pm20) REVERT: B 224 ASN cc_start: 0.7045 (m110) cc_final: 0.6068 (t0) REVERT: B 241 TYR cc_start: 0.8283 (t80) cc_final: 0.8011 (t80) REVERT: B 259 TYR cc_start: 0.8103 (t80) cc_final: 0.7153 (t80) REVERT: B 452 ASP cc_start: 0.7138 (t0) cc_final: 0.6934 (t70) REVERT: C 122 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8033 (ttp-110) REVERT: C 164 ASP cc_start: 0.7387 (m-30) cc_final: 0.6914 (p0) REVERT: C 209 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7645 (pt0) REVERT: C 224 ASN cc_start: 0.7124 (m110) cc_final: 0.6154 (t0) REVERT: C 320 LYS cc_start: 0.8181 (tttp) cc_final: 0.7723 (ttpt) REVERT: D 164 ASP cc_start: 0.7383 (m-30) cc_final: 0.7000 (p0) REVERT: D 224 ASN cc_start: 0.7082 (m110) cc_final: 0.6257 (t0) REVERT: D 285 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7809 (mm-30) REVERT: D 320 LYS cc_start: 0.8153 (tttp) cc_final: 0.7768 (ttpt) REVERT: E 224 ASN cc_start: 0.7089 (m110) cc_final: 0.6070 (t0) REVERT: E 259 TYR cc_start: 0.8273 (t80) cc_final: 0.7566 (t80) REVERT: F 164 ASP cc_start: 0.7255 (m-30) cc_final: 0.6874 (p0) REVERT: F 241 TYR cc_start: 0.8436 (t80) cc_final: 0.7949 (t80) REVERT: F 416 LYS cc_start: 0.8289 (tptm) cc_final: 0.7239 (mptt) REVERT: F 438 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7327 (tpp-160) outliers start: 1 outliers final: 2 residues processed: 341 average time/residue: 0.5919 time to fit residues: 227.5926 Evaluate side-chains 264 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 325 GLN D 325 GLN F 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.174484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154012 restraints weight = 20159.119| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.86 r_work: 0.3740 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18894 Z= 0.137 Angle : 0.544 6.179 25674 Z= 0.287 Chirality : 0.045 0.151 2856 Planarity : 0.004 0.036 3318 Dihedral : 10.561 87.257 2752 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.08 % Allowed : 9.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2334 helix: -0.38 (0.24), residues: 438 sheet: -0.31 (0.22), residues: 432 loop : 0.16 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 265 TYR 0.013 0.001 TYR F 69 PHE 0.023 0.002 PHE D 211 TRP 0.019 0.002 TRP E 144 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00320 (18894) covalent geometry : angle 0.54367 (25674) hydrogen bonds : bond 0.04339 ( 447) hydrogen bonds : angle 5.88238 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7883 (m-80) cc_final: 0.7627 (m-80) REVERT: A 123 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7627 (mppt) REVERT: A 184 MET cc_start: 0.6739 (ppp) cc_final: 0.6384 (ppp) REVERT: A 377 GLN cc_start: 0.7851 (mt0) cc_final: 0.7500 (mt0) REVERT: A 416 LYS cc_start: 0.8267 (tptm) cc_final: 0.6931 (mptt) REVERT: A 438 ARG cc_start: 0.7468 (mmt-90) cc_final: 0.7147 (tpp-160) REVERT: B 123 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7566 (mppt) REVERT: B 197 GLU cc_start: 0.7654 (pt0) cc_final: 0.7034 (pm20) REVERT: B 224 ASN cc_start: 0.6998 (m110) cc_final: 0.6055 (t0) REVERT: B 320 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7587 (tttm) REVERT: B 421 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.6231 (t-170) REVERT: C 164 ASP cc_start: 0.7295 (m-30) cc_final: 0.6871 (p0) REVERT: C 224 ASN cc_start: 0.7098 (m110) cc_final: 0.6151 (t0) REVERT: C 285 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7526 (mt-10) REVERT: C 320 LYS cc_start: 0.8143 (tttp) cc_final: 0.7685 (ttpt) REVERT: C 325 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6622 (mp-120) REVERT: D 224 ASN cc_start: 0.7073 (m110) cc_final: 0.6178 (t0) REVERT: D 285 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7564 (mt-10) REVERT: D 320 LYS cc_start: 0.8149 (tttp) cc_final: 0.7632 (ttpt) REVERT: D 325 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6641 (mp-120) REVERT: E 220 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: E 224 ASN cc_start: 0.7013 (m110) cc_final: 0.6054 (t0) REVERT: E 259 TYR cc_start: 0.8362 (t80) cc_final: 0.7602 (t80) REVERT: E 452 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7032 (t0) REVERT: F 111 PHE cc_start: 0.7926 (m-80) cc_final: 0.7716 (m-80) REVERT: F 164 ASP cc_start: 0.7147 (m-30) cc_final: 0.6753 (p0) REVERT: F 241 TYR cc_start: 0.8500 (t80) cc_final: 0.7957 (t80) REVERT: F 416 LYS cc_start: 0.8273 (tptm) cc_final: 0.6997 (mptt) REVERT: F 438 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7115 (tpp-160) outliers start: 41 outliers final: 21 residues processed: 286 average time/residue: 0.5806 time to fit residues: 187.5850 Evaluate side-chains 267 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 141 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 214 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154264 restraints weight = 20327.656| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.75 r_work: 0.3740 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18894 Z= 0.156 Angle : 0.545 6.302 25674 Z= 0.288 Chirality : 0.045 0.147 2856 Planarity : 0.004 0.028 3318 Dihedral : 9.672 89.673 2748 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.44 % Allowed : 12.09 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2334 helix: -0.29 (0.24), residues: 438 sheet: -0.60 (0.22), residues: 444 loop : 0.23 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 110 TYR 0.018 0.001 TYR E 69 PHE 0.025 0.002 PHE D 211 TRP 0.012 0.002 TRP E 144 HIS 0.004 0.001 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00369 (18894) covalent geometry : angle 0.54533 (25674) hydrogen bonds : bond 0.03950 ( 447) hydrogen bonds : angle 5.65071 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7796 (m-80) cc_final: 0.7571 (m-80) REVERT: A 123 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7688 (mppt) REVERT: A 224 ASN cc_start: 0.7283 (m110) cc_final: 0.6341 (t0) REVERT: A 241 TYR cc_start: 0.8457 (t80) cc_final: 0.8159 (t80) REVERT: A 325 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6509 (mp-120) REVERT: A 414 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7699 (tpp80) REVERT: A 416 LYS cc_start: 0.8270 (tptm) cc_final: 0.7045 (mptt) REVERT: A 438 ARG cc_start: 0.7350 (mmt-90) cc_final: 0.7116 (tpp-160) REVERT: A 452 ASP cc_start: 0.7108 (t0) cc_final: 0.6786 (t0) REVERT: B 64 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: B 123 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7594 (mppt) REVERT: B 125 ASP cc_start: 0.6732 (p0) cc_final: 0.6120 (m-30) REVERT: B 197 GLU cc_start: 0.7716 (pt0) cc_final: 0.7070 (pm20) REVERT: B 224 ASN cc_start: 0.7012 (m110) cc_final: 0.6127 (t0) REVERT: B 259 TYR cc_start: 0.8180 (t80) cc_final: 0.7120 (t80) REVERT: B 320 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7594 (tttm) REVERT: B 325 GLN cc_start: 0.7221 (mp-120) cc_final: 0.7013 (mm110) REVERT: B 452 ASP cc_start: 0.7225 (t0) cc_final: 0.6982 (t0) REVERT: C 224 ASN cc_start: 0.7047 (m110) cc_final: 0.6088 (t0) REVERT: C 285 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 320 LYS cc_start: 0.8122 (tttp) cc_final: 0.7691 (ttpt) REVERT: C 456 GLN cc_start: 0.6759 (tp40) cc_final: 0.6488 (mm110) REVERT: D 224 ASN cc_start: 0.7089 (m110) cc_final: 0.6262 (t0) REVERT: D 285 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 320 LYS cc_start: 0.8084 (tttp) cc_final: 0.7661 (ttpt) REVERT: D 456 GLN cc_start: 0.7030 (tp40) cc_final: 0.6647 (mm110) REVERT: E 224 ASN cc_start: 0.7029 (m110) cc_final: 0.6057 (t0) REVERT: E 259 TYR cc_start: 0.8328 (t80) cc_final: 0.7658 (t80) REVERT: E 416 LYS cc_start: 0.8201 (tptm) cc_final: 0.6930 (mptt) REVERT: F 64 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6071 (pp20) REVERT: F 125 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: F 164 ASP cc_start: 0.7101 (m-30) cc_final: 0.6727 (p0) REVERT: F 224 ASN cc_start: 0.7269 (m110) cc_final: 0.6360 (t0) REVERT: F 241 TYR cc_start: 0.8574 (t80) cc_final: 0.7921 (t80) REVERT: F 325 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6566 (mp-120) REVERT: F 416 LYS cc_start: 0.8298 (tptm) cc_final: 0.7072 (mptt) REVERT: F 438 ARG cc_start: 0.7374 (mmt-90) cc_final: 0.7127 (tpp-160) outliers start: 48 outliers final: 21 residues processed: 278 average time/residue: 0.5616 time to fit residues: 176.6486 Evaluate side-chains 269 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 139 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 175 optimal weight: 0.0770 chunk 216 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 243 ASN F 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154240 restraints weight = 20254.828| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.74 r_work: 0.3741 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18894 Z= 0.152 Angle : 0.539 6.280 25674 Z= 0.285 Chirality : 0.044 0.147 2856 Planarity : 0.003 0.029 3318 Dihedral : 9.117 86.270 2748 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.00 % Allowed : 13.77 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2334 helix: -0.21 (0.24), residues: 438 sheet: -0.68 (0.22), residues: 444 loop : 0.20 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 110 TYR 0.012 0.001 TYR C 259 PHE 0.026 0.002 PHE D 211 TRP 0.009 0.002 TRP E 144 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00360 (18894) covalent geometry : angle 0.53920 (25674) hydrogen bonds : bond 0.03651 ( 447) hydrogen bonds : angle 5.57014 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7830 (m-80) cc_final: 0.7612 (m-80) REVERT: A 123 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7667 (mppt) REVERT: A 184 MET cc_start: 0.6743 (ppp) cc_final: 0.6375 (ppp) REVERT: A 224 ASN cc_start: 0.7258 (m110) cc_final: 0.6331 (t0) REVERT: A 241 TYR cc_start: 0.8544 (t80) cc_final: 0.8080 (t80) REVERT: A 414 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7727 (tpp80) REVERT: A 416 LYS cc_start: 0.8277 (tptm) cc_final: 0.7017 (mptt) REVERT: A 438 ARG cc_start: 0.7333 (mmt-90) cc_final: 0.7088 (tpp-160) REVERT: B 64 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6576 (pp20) REVERT: B 123 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7624 (mppt) REVERT: B 125 ASP cc_start: 0.6727 (p0) cc_final: 0.6104 (m-30) REVERT: B 224 ASN cc_start: 0.6995 (m110) cc_final: 0.6124 (t0) REVERT: B 259 TYR cc_start: 0.8190 (t80) cc_final: 0.7142 (t80) REVERT: B 320 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7574 (tttm) REVERT: B 325 GLN cc_start: 0.7232 (mp-120) cc_final: 0.7022 (mm110) REVERT: B 416 LYS cc_start: 0.8159 (tptm) cc_final: 0.6917 (mptt) REVERT: B 421 HIS cc_start: 0.6038 (t-170) cc_final: 0.5822 (t-170) REVERT: C 224 ASN cc_start: 0.7036 (m110) cc_final: 0.6107 (t0) REVERT: C 285 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 299 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7148 (p0) REVERT: C 320 LYS cc_start: 0.8130 (tttp) cc_final: 0.7705 (ttpt) REVERT: C 325 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6856 (mm110) REVERT: C 456 GLN cc_start: 0.6803 (tp40) cc_final: 0.6524 (mm110) REVERT: D 224 ASN cc_start: 0.7101 (m110) cc_final: 0.6266 (t0) REVERT: D 285 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 320 LYS cc_start: 0.8077 (tttp) cc_final: 0.7672 (ttpt) REVERT: D 325 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6877 (mm110) REVERT: D 456 GLN cc_start: 0.7042 (tp40) cc_final: 0.6645 (mm110) REVERT: E 64 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: E 224 ASN cc_start: 0.7019 (m110) cc_final: 0.6056 (t0) REVERT: E 265 ARG cc_start: 0.8659 (ptm160) cc_final: 0.8270 (ptp-170) REVERT: E 416 LYS cc_start: 0.8190 (tptm) cc_final: 0.6933 (mptt) REVERT: E 452 ASP cc_start: 0.7180 (t0) cc_final: 0.6514 (t0) REVERT: F 64 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6045 (pp20) REVERT: F 123 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7704 (mppt) REVERT: F 125 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: F 164 ASP cc_start: 0.7111 (m-30) cc_final: 0.6715 (p0) REVERT: F 224 ASN cc_start: 0.7250 (m110) cc_final: 0.6319 (t0) REVERT: F 241 TYR cc_start: 0.8603 (t80) cc_final: 0.7989 (t80) REVERT: F 416 LYS cc_start: 0.8308 (tptm) cc_final: 0.7030 (mptt) outliers start: 59 outliers final: 28 residues processed: 283 average time/residue: 0.6004 time to fit residues: 192.5005 Evaluate side-chains 274 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 127 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153609 restraints weight = 20154.072| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.73 r_work: 0.3736 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18894 Z= 0.159 Angle : 0.540 6.374 25674 Z= 0.287 Chirality : 0.044 0.146 2856 Planarity : 0.003 0.030 3318 Dihedral : 8.686 77.467 2748 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.00 % Allowed : 14.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2334 helix: -0.14 (0.25), residues: 438 sheet: -0.70 (0.22), residues: 444 loop : 0.18 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 110 TYR 0.021 0.001 TYR F 69 PHE 0.023 0.002 PHE D 211 TRP 0.008 0.002 TRP E 144 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00376 (18894) covalent geometry : angle 0.54049 (25674) hydrogen bonds : bond 0.03559 ( 447) hydrogen bonds : angle 5.53563 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7863 (m-80) cc_final: 0.7647 (m-80) REVERT: A 123 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7674 (mppt) REVERT: A 224 ASN cc_start: 0.7270 (m110) cc_final: 0.6340 (t0) REVERT: A 241 TYR cc_start: 0.8616 (t80) cc_final: 0.7927 (t80) REVERT: A 414 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7709 (tpp80) REVERT: A 416 LYS cc_start: 0.8314 (tptm) cc_final: 0.7033 (mptt) REVERT: A 438 ARG cc_start: 0.7323 (mmt-90) cc_final: 0.7066 (tpp-160) REVERT: B 64 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: B 123 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7614 (mppt) REVERT: B 125 ASP cc_start: 0.6822 (p0) cc_final: 0.6190 (m-30) REVERT: B 184 MET cc_start: 0.6371 (mtm) cc_final: 0.6152 (ptt) REVERT: B 224 ASN cc_start: 0.6993 (m110) cc_final: 0.6088 (t0) REVERT: B 259 TYR cc_start: 0.8237 (t80) cc_final: 0.7186 (t80) REVERT: B 320 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7574 (tttm) REVERT: B 416 LYS cc_start: 0.8125 (tptm) cc_final: 0.6869 (mptt) REVERT: C 224 ASN cc_start: 0.7054 (m110) cc_final: 0.6101 (t0) REVERT: C 243 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8819 (p0) REVERT: C 285 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 299 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7180 (p0) REVERT: C 320 LYS cc_start: 0.8132 (tttp) cc_final: 0.7703 (ttpt) REVERT: C 325 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6831 (mm110) REVERT: C 416 LYS cc_start: 0.8303 (tptm) cc_final: 0.7156 (mptt) REVERT: C 456 GLN cc_start: 0.6861 (tp40) cc_final: 0.6522 (mm110) REVERT: D 224 ASN cc_start: 0.7100 (m110) cc_final: 0.6273 (t0) REVERT: D 285 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7642 (mt-10) REVERT: D 320 LYS cc_start: 0.8126 (tttp) cc_final: 0.7718 (ttpt) REVERT: D 325 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6855 (mm110) REVERT: D 384 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: D 456 GLN cc_start: 0.7019 (tp40) cc_final: 0.6566 (mm110) REVERT: E 64 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: E 123 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7713 (mppt) REVERT: E 224 ASN cc_start: 0.7015 (m110) cc_final: 0.6046 (t0) REVERT: E 265 ARG cc_start: 0.8662 (ptm160) cc_final: 0.8307 (ptp-170) REVERT: E 416 LYS cc_start: 0.8092 (tptm) cc_final: 0.6913 (mptt) REVERT: E 452 ASP cc_start: 0.7154 (t0) cc_final: 0.6509 (t0) REVERT: F 64 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6000 (pp20) REVERT: F 123 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7708 (mppt) REVERT: F 125 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: F 164 ASP cc_start: 0.7109 (m-30) cc_final: 0.6699 (p0) REVERT: F 224 ASN cc_start: 0.7268 (m110) cc_final: 0.6362 (t0) REVERT: F 241 TYR cc_start: 0.8615 (t80) cc_final: 0.8412 (t80) REVERT: F 416 LYS cc_start: 0.8303 (tptm) cc_final: 0.7028 (mptt) outliers start: 59 outliers final: 32 residues processed: 281 average time/residue: 0.5739 time to fit residues: 182.5480 Evaluate side-chains 279 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 42 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.172785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152991 restraints weight = 20161.719| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.73 r_work: 0.3728 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18894 Z= 0.171 Angle : 0.553 6.505 25674 Z= 0.294 Chirality : 0.045 0.151 2856 Planarity : 0.004 0.050 3318 Dihedral : 8.528 70.760 2748 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.40 % Allowed : 14.94 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2334 helix: -0.11 (0.25), residues: 438 sheet: -0.70 (0.22), residues: 444 loop : 0.14 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 220 TYR 0.012 0.001 TYR C 259 PHE 0.026 0.002 PHE D 211 TRP 0.008 0.002 TRP C 275 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00406 (18894) covalent geometry : angle 0.55336 (25674) hydrogen bonds : bond 0.03574 ( 447) hydrogen bonds : angle 5.55277 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7859 (m-80) cc_final: 0.7653 (m-80) REVERT: A 123 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7692 (mppt) REVERT: A 184 MET cc_start: 0.6792 (ppp) cc_final: 0.6444 (ppp) REVERT: A 224 ASN cc_start: 0.7256 (m110) cc_final: 0.6312 (t0) REVERT: A 241 TYR cc_start: 0.8623 (t80) cc_final: 0.7906 (t80) REVERT: A 414 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (tpp80) REVERT: A 416 LYS cc_start: 0.8291 (tptm) cc_final: 0.7029 (mptt) REVERT: A 438 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.7076 (tpp-160) REVERT: B 64 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: B 123 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7648 (mppt) REVERT: B 125 ASP cc_start: 0.6832 (p0) cc_final: 0.6196 (m-30) REVERT: B 224 ASN cc_start: 0.6997 (m110) cc_final: 0.6107 (t0) REVERT: B 259 TYR cc_start: 0.8251 (t80) cc_final: 0.7295 (t80) REVERT: B 320 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7639 (tttm) REVERT: B 416 LYS cc_start: 0.8041 (tptm) cc_final: 0.6739 (mptt) REVERT: C 224 ASN cc_start: 0.7058 (m110) cc_final: 0.6108 (t0) REVERT: C 285 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 299 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7186 (p0) REVERT: C 320 LYS cc_start: 0.8163 (tttp) cc_final: 0.7726 (ttpt) REVERT: C 416 LYS cc_start: 0.8367 (tptm) cc_final: 0.7205 (mptt) REVERT: C 452 ASP cc_start: 0.7241 (t0) cc_final: 0.6858 (t0) REVERT: C 456 GLN cc_start: 0.6877 (tp40) cc_final: 0.6554 (mm110) REVERT: D 224 ASN cc_start: 0.7107 (m110) cc_final: 0.6265 (t0) REVERT: D 285 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 320 LYS cc_start: 0.8151 (tttp) cc_final: 0.7742 (ttpt) REVERT: D 397 GLU cc_start: 0.5960 (pm20) cc_final: 0.5597 (pp20) REVERT: D 452 ASP cc_start: 0.7218 (t0) cc_final: 0.6814 (t0) REVERT: D 456 GLN cc_start: 0.7015 (tp40) cc_final: 0.6579 (mm110) REVERT: E 64 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: E 123 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7716 (mppt) REVERT: E 224 ASN cc_start: 0.7025 (m110) cc_final: 0.6042 (t0) REVERT: E 264 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: E 265 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8480 (ptp-170) REVERT: E 416 LYS cc_start: 0.8116 (tptm) cc_final: 0.6896 (mptt) REVERT: E 452 ASP cc_start: 0.7152 (t0) cc_final: 0.6518 (t0) REVERT: F 64 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6020 (pp20) REVERT: F 123 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7689 (mppt) REVERT: F 125 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: F 164 ASP cc_start: 0.7164 (m-30) cc_final: 0.6741 (p0) REVERT: F 224 ASN cc_start: 0.7259 (m110) cc_final: 0.6341 (t0) REVERT: F 241 TYR cc_start: 0.8604 (t80) cc_final: 0.8394 (t80) REVERT: F 416 LYS cc_start: 0.8301 (tptm) cc_final: 0.7017 (mptt) outliers start: 67 outliers final: 37 residues processed: 281 average time/residue: 0.5431 time to fit residues: 173.5837 Evaluate side-chains 275 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 1.9990 chunk 204 optimal weight: 0.0020 chunk 134 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 167 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158256 restraints weight = 20243.140| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.73 r_work: 0.3784 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18894 Z= 0.106 Angle : 0.505 5.867 25674 Z= 0.267 Chirality : 0.043 0.135 2856 Planarity : 0.003 0.034 3318 Dihedral : 7.399 55.845 2748 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.29 % Allowed : 16.41 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2334 helix: 0.05 (0.25), residues: 438 sheet: -0.57 (0.22), residues: 438 loop : 0.20 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 110 TYR 0.013 0.001 TYR D 259 PHE 0.025 0.001 PHE D 211 TRP 0.008 0.001 TRP E 144 HIS 0.002 0.000 HIS D 248 Details of bonding type rmsd covalent geometry : bond 0.00251 (18894) covalent geometry : angle 0.50548 (25674) hydrogen bonds : bond 0.03030 ( 447) hydrogen bonds : angle 5.33211 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6104 (tt0) REVERT: A 123 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7608 (mppt) REVERT: A 184 MET cc_start: 0.6698 (ppp) cc_final: 0.6235 (ppp) REVERT: A 224 ASN cc_start: 0.7280 (m110) cc_final: 0.6336 (t0) REVERT: A 241 TYR cc_start: 0.8470 (t80) cc_final: 0.7921 (t80) REVERT: A 416 LYS cc_start: 0.8198 (tptm) cc_final: 0.6963 (mptt) REVERT: A 438 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.7042 (tpp-160) REVERT: B 64 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: B 123 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7585 (mppt) REVERT: B 224 ASN cc_start: 0.6954 (m110) cc_final: 0.6057 (t0) REVERT: B 259 TYR cc_start: 0.8093 (t80) cc_final: 0.7418 (t80) REVERT: B 320 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7711 (tttm) REVERT: B 363 ILE cc_start: 0.8089 (mt) cc_final: 0.7677 (mp) REVERT: B 416 LYS cc_start: 0.7998 (tptm) cc_final: 0.6770 (mptt) REVERT: C 224 ASN cc_start: 0.7018 (m110) cc_final: 0.6085 (t0) REVERT: C 285 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7854 (mt-10) REVERT: C 299 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7143 (p0) REVERT: C 320 LYS cc_start: 0.7971 (tttp) cc_final: 0.7590 (ttpt) REVERT: C 325 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6795 (mm110) REVERT: C 416 LYS cc_start: 0.8234 (tptm) cc_final: 0.7103 (mptt) REVERT: C 452 ASP cc_start: 0.7164 (t0) cc_final: 0.6877 (t0) REVERT: C 456 GLN cc_start: 0.6875 (tp40) cc_final: 0.6573 (mm110) REVERT: D 122 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7976 (ttp-110) REVERT: D 224 ASN cc_start: 0.7100 (m110) cc_final: 0.6241 (t0) REVERT: D 285 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 320 LYS cc_start: 0.7968 (tttp) cc_final: 0.7632 (ttpt) REVERT: D 325 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6816 (mm110) REVERT: D 452 ASP cc_start: 0.7177 (t0) cc_final: 0.6886 (t0) REVERT: D 456 GLN cc_start: 0.7057 (tp40) cc_final: 0.6651 (mm110) REVERT: E 64 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6450 (tt0) REVERT: E 224 ASN cc_start: 0.7008 (m110) cc_final: 0.6040 (t0) REVERT: E 259 TYR cc_start: 0.8283 (t80) cc_final: 0.7664 (t80) REVERT: E 416 LYS cc_start: 0.8072 (tptm) cc_final: 0.6879 (mptt) REVERT: E 452 ASP cc_start: 0.7200 (t70) cc_final: 0.6550 (t0) REVERT: F 64 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6072 (tt0) REVERT: F 125 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: F 224 ASN cc_start: 0.7264 (m110) cc_final: 0.6336 (t0) REVERT: F 241 TYR cc_start: 0.8456 (t80) cc_final: 0.8237 (t80) REVERT: F 416 LYS cc_start: 0.8198 (tptm) cc_final: 0.6965 (mptt) outliers start: 45 outliers final: 24 residues processed: 304 average time/residue: 0.5678 time to fit residues: 195.1110 Evaluate side-chains 279 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 0.1980 chunk 86 optimal weight: 0.0050 chunk 107 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 243 ASN E 421 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.174163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153531 restraints weight = 20004.819| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.86 r_work: 0.3725 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18894 Z= 0.122 Angle : 0.523 7.397 25674 Z= 0.277 Chirality : 0.043 0.136 2856 Planarity : 0.003 0.056 3318 Dihedral : 7.316 56.119 2748 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.44 % Allowed : 17.28 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.17), residues: 2334 helix: 0.04 (0.24), residues: 438 sheet: -0.63 (0.22), residues: 438 loop : 0.22 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 110 TYR 0.014 0.001 TYR D 259 PHE 0.027 0.002 PHE D 211 TRP 0.007 0.001 TRP D 275 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00287 (18894) covalent geometry : angle 0.52329 (25674) hydrogen bonds : bond 0.03103 ( 447) hydrogen bonds : angle 5.34219 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.696 Fit side-chains REVERT: A 64 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5970 (tt0) REVERT: A 123 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7602 (mppt) REVERT: A 184 MET cc_start: 0.6693 (ppp) cc_final: 0.6260 (ppp) REVERT: A 224 ASN cc_start: 0.7166 (m110) cc_final: 0.6198 (t0) REVERT: A 416 LYS cc_start: 0.8275 (tptm) cc_final: 0.7027 (mptt) REVERT: A 438 ARG cc_start: 0.7328 (mmt-90) cc_final: 0.7095 (tpp-160) REVERT: B 64 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: B 123 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7545 (mppt) REVERT: B 125 ASP cc_start: 0.6885 (p0) cc_final: 0.6275 (m-30) REVERT: B 224 ASN cc_start: 0.6981 (m110) cc_final: 0.5942 (t0) REVERT: B 259 TYR cc_start: 0.8190 (t80) cc_final: 0.7347 (t80) REVERT: B 320 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7738 (tttm) REVERT: B 363 ILE cc_start: 0.8157 (mt) cc_final: 0.7725 (mp) REVERT: B 416 LYS cc_start: 0.7991 (tptm) cc_final: 0.6701 (mptt) REVERT: C 89 GLN cc_start: 0.6297 (tp40) cc_final: 0.6005 (tt0) REVERT: C 224 ASN cc_start: 0.6938 (m110) cc_final: 0.5966 (t0) REVERT: C 243 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8628 (p0) REVERT: C 299 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7165 (p0) REVERT: C 320 LYS cc_start: 0.8003 (tttp) cc_final: 0.7613 (ttpt) REVERT: C 325 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6901 (mm110) REVERT: C 416 LYS cc_start: 0.8192 (tptm) cc_final: 0.7001 (mptt) REVERT: C 452 ASP cc_start: 0.7170 (t0) cc_final: 0.6943 (t0) REVERT: C 456 GLN cc_start: 0.6904 (tp40) cc_final: 0.6586 (mm110) REVERT: D 224 ASN cc_start: 0.7046 (m110) cc_final: 0.6133 (t0) REVERT: D 285 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7619 (mt-10) REVERT: D 299 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7197 (p0) REVERT: D 320 LYS cc_start: 0.8027 (tttp) cc_final: 0.7615 (ttpt) REVERT: D 325 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6886 (mm110) REVERT: D 452 ASP cc_start: 0.7142 (t0) cc_final: 0.6890 (t0) REVERT: D 456 GLN cc_start: 0.6969 (tp40) cc_final: 0.6548 (mm110) REVERT: E 64 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6349 (tt0) REVERT: E 224 ASN cc_start: 0.6993 (m110) cc_final: 0.5997 (t0) REVERT: E 259 TYR cc_start: 0.8343 (t80) cc_final: 0.7726 (t80) REVERT: E 363 ILE cc_start: 0.8037 (mt) cc_final: 0.7811 (mt) REVERT: E 416 LYS cc_start: 0.8137 (tptm) cc_final: 0.6907 (mptt) REVERT: E 452 ASP cc_start: 0.7259 (t70) cc_final: 0.6634 (t0) REVERT: F 64 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6007 (tt0) REVERT: F 125 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: F 224 ASN cc_start: 0.7170 (m110) cc_final: 0.6232 (t0) REVERT: F 241 TYR cc_start: 0.8429 (t80) cc_final: 0.8225 (t80) REVERT: F 416 LYS cc_start: 0.8271 (tptm) cc_final: 0.7037 (mptt) outliers start: 48 outliers final: 28 residues processed: 288 average time/residue: 0.5942 time to fit residues: 193.1532 Evaluate side-chains 276 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 98 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN E 421 HIS F 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151854 restraints weight = 20016.753| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.86 r_work: 0.3733 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18894 Z= 0.149 Angle : 0.552 7.295 25674 Z= 0.292 Chirality : 0.044 0.137 2856 Planarity : 0.004 0.089 3318 Dihedral : 7.513 56.691 2748 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.64 % Allowed : 17.68 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2334 helix: -0.03 (0.25), residues: 438 sheet: -0.61 (0.22), residues: 438 loop : 0.17 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.012 0.001 TYR D 259 PHE 0.026 0.002 PHE D 211 TRP 0.008 0.002 TRP D 275 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00355 (18894) covalent geometry : angle 0.55230 (25674) hydrogen bonds : bond 0.03259 ( 447) hydrogen bonds : angle 5.44779 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.747 Fit side-chains REVERT: A 64 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5951 (tt0) REVERT: A 123 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7656 (mppt) REVERT: A 224 ASN cc_start: 0.7176 (m110) cc_final: 0.6189 (t0) REVERT: A 241 TYR cc_start: 0.8417 (t80) cc_final: 0.8002 (t80) REVERT: A 416 LYS cc_start: 0.8299 (tptm) cc_final: 0.7037 (mptt) REVERT: A 438 ARG cc_start: 0.7373 (mmt-90) cc_final: 0.7123 (tpp-160) REVERT: B 64 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: B 123 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7558 (mppt) REVERT: B 125 ASP cc_start: 0.6890 (p0) cc_final: 0.6314 (m-30) REVERT: B 184 MET cc_start: 0.6462 (mtm) cc_final: 0.6007 (ptt) REVERT: B 224 ASN cc_start: 0.6989 (m110) cc_final: 0.5940 (t0) REVERT: B 259 TYR cc_start: 0.8268 (t80) cc_final: 0.7304 (t80) REVERT: B 320 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7732 (tttm) REVERT: B 414 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7549 (mpp80) REVERT: B 416 LYS cc_start: 0.8007 (tptm) cc_final: 0.6786 (mptt) REVERT: C 89 GLN cc_start: 0.6311 (tp40) cc_final: 0.5995 (tt0) REVERT: C 224 ASN cc_start: 0.6980 (m110) cc_final: 0.5964 (t0) REVERT: C 299 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7201 (p0) REVERT: C 320 LYS cc_start: 0.8040 (tttp) cc_final: 0.7623 (ttpt) REVERT: C 416 LYS cc_start: 0.8245 (tptm) cc_final: 0.7044 (mptt) REVERT: C 452 ASP cc_start: 0.7183 (t0) cc_final: 0.6957 (t0) REVERT: C 456 GLN cc_start: 0.6890 (tp40) cc_final: 0.6560 (mm110) REVERT: D 224 ASN cc_start: 0.7033 (m110) cc_final: 0.6166 (t0) REVERT: D 285 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7551 (mt-10) REVERT: D 299 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7216 (p0) REVERT: D 320 LYS cc_start: 0.8078 (tttp) cc_final: 0.7634 (ttpt) REVERT: D 325 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6975 (mm110) REVERT: D 456 GLN cc_start: 0.6936 (tp40) cc_final: 0.6520 (mm110) REVERT: E 64 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6343 (tt0) REVERT: E 125 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6400 (m-30) REVERT: E 224 ASN cc_start: 0.7043 (m110) cc_final: 0.6011 (t0) REVERT: E 259 TYR cc_start: 0.8347 (t80) cc_final: 0.7721 (t80) REVERT: E 363 ILE cc_start: 0.8145 (mt) cc_final: 0.7757 (mp) REVERT: E 416 LYS cc_start: 0.8172 (tptm) cc_final: 0.6917 (mptt) REVERT: E 452 ASP cc_start: 0.7242 (t70) cc_final: 0.6605 (t0) REVERT: F 64 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: F 125 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6489 (m-30) REVERT: F 224 ASN cc_start: 0.7178 (m110) cc_final: 0.6204 (t0) REVERT: F 241 TYR cc_start: 0.8484 (t80) cc_final: 0.8282 (t80) REVERT: F 416 LYS cc_start: 0.8292 (tptm) cc_final: 0.7035 (mptt) outliers start: 52 outliers final: 30 residues processed: 273 average time/residue: 0.5934 time to fit residues: 183.5520 Evaluate side-chains 274 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN C 325 GLN E 421 HIS F 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152726 restraints weight = 20124.413| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.87 r_work: 0.3745 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18894 Z= 0.132 Angle : 0.543 7.112 25674 Z= 0.288 Chirality : 0.044 0.137 2856 Planarity : 0.003 0.032 3318 Dihedral : 7.339 57.222 2748 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.49 % Allowed : 17.94 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2334 helix: -0.04 (0.24), residues: 438 sheet: -0.59 (0.23), residues: 438 loop : 0.17 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.013 0.001 TYR D 259 PHE 0.028 0.002 PHE D 211 TRP 0.007 0.002 TRP D 275 HIS 0.003 0.001 HIS D 248 Details of bonding type rmsd covalent geometry : bond 0.00314 (18894) covalent geometry : angle 0.54310 (25674) hydrogen bonds : bond 0.03145 ( 447) hydrogen bonds : angle 5.43553 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.726 Fit side-chains REVERT: A 64 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5932 (tt0) REVERT: A 123 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7616 (mppt) REVERT: A 184 MET cc_start: 0.6782 (ppp) cc_final: 0.6472 (ppp) REVERT: A 224 ASN cc_start: 0.7147 (m110) cc_final: 0.6164 (t0) REVERT: A 241 TYR cc_start: 0.8386 (t80) cc_final: 0.7956 (t80) REVERT: A 377 GLN cc_start: 0.7865 (mt0) cc_final: 0.7521 (mt0) REVERT: A 416 LYS cc_start: 0.8267 (tptm) cc_final: 0.7014 (mptt) REVERT: A 438 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.7114 (tpp-160) REVERT: B 64 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: B 123 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7533 (mppt) REVERT: B 125 ASP cc_start: 0.6897 (p0) cc_final: 0.6317 (m-30) REVERT: B 184 MET cc_start: 0.6482 (mtm) cc_final: 0.5995 (ptt) REVERT: B 224 ASN cc_start: 0.6956 (m110) cc_final: 0.5950 (t0) REVERT: B 259 TYR cc_start: 0.8232 (t80) cc_final: 0.7338 (t80) REVERT: B 320 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7425 (ttpt) REVERT: B 414 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7489 (mpp80) REVERT: B 416 LYS cc_start: 0.7994 (tptm) cc_final: 0.6707 (mptt) REVERT: C 89 GLN cc_start: 0.6330 (tp40) cc_final: 0.6013 (tt0) REVERT: C 224 ASN cc_start: 0.6963 (m110) cc_final: 0.5935 (t0) REVERT: C 299 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7174 (p0) REVERT: C 320 LYS cc_start: 0.7998 (tttp) cc_final: 0.7598 (ttpt) REVERT: C 325 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6817 (mp-120) REVERT: C 416 LYS cc_start: 0.8242 (tptm) cc_final: 0.7034 (mptt) REVERT: C 452 ASP cc_start: 0.7232 (t0) cc_final: 0.7012 (t0) REVERT: C 456 GLN cc_start: 0.6877 (tp40) cc_final: 0.6549 (mm110) REVERT: D 224 ASN cc_start: 0.7035 (m110) cc_final: 0.6082 (t0) REVERT: D 299 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7224 (p0) REVERT: D 320 LYS cc_start: 0.8041 (tttp) cc_final: 0.7610 (ttpt) REVERT: D 325 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6962 (mm110) REVERT: D 397 GLU cc_start: 0.5831 (pm20) cc_final: 0.5596 (pp20) REVERT: D 456 GLN cc_start: 0.6951 (tp40) cc_final: 0.6545 (mm110) REVERT: E 64 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: E 125 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6408 (m-30) REVERT: E 224 ASN cc_start: 0.6994 (m110) cc_final: 0.5938 (t0) REVERT: E 259 TYR cc_start: 0.8346 (t80) cc_final: 0.7712 (t80) REVERT: E 363 ILE cc_start: 0.8067 (mt) cc_final: 0.7772 (mt) REVERT: E 416 LYS cc_start: 0.8137 (tptm) cc_final: 0.6887 (mptt) REVERT: E 452 ASP cc_start: 0.7232 (t70) cc_final: 0.6597 (t0) REVERT: F 64 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5913 (tt0) REVERT: F 125 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6486 (m-30) REVERT: F 224 ASN cc_start: 0.7189 (m110) cc_final: 0.6217 (t0) REVERT: F 241 TYR cc_start: 0.8421 (t80) cc_final: 0.8219 (t80) REVERT: F 416 LYS cc_start: 0.8285 (tptm) cc_final: 0.7016 (mptt) outliers start: 49 outliers final: 32 residues processed: 272 average time/residue: 0.5910 time to fit residues: 181.9872 Evaluate side-chains 278 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 211 PHE Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 163 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN C 325 GLN E 421 HIS F 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152315 restraints weight = 20104.059| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.87 r_work: 0.3738 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18894 Z= 0.141 Angle : 0.554 7.131 25674 Z= 0.293 Chirality : 0.044 0.136 2856 Planarity : 0.003 0.032 3318 Dihedral : 7.356 57.363 2748 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.54 % Allowed : 18.04 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2334 helix: -0.05 (0.25), residues: 438 sheet: -0.57 (0.23), residues: 438 loop : 0.16 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 110 TYR 0.013 0.001 TYR D 259 PHE 0.027 0.002 PHE D 211 TRP 0.007 0.002 TRP D 275 HIS 0.003 0.001 HIS D 248 Details of bonding type rmsd covalent geometry : bond 0.00335 (18894) covalent geometry : angle 0.55449 (25674) hydrogen bonds : bond 0.03182 ( 447) hydrogen bonds : angle 5.45188 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6243.54 seconds wall clock time: 107 minutes 14.36 seconds (6434.36 seconds total)