Starting phenix.real_space_refine on Mon Jun 16 09:30:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pn2_17768/06_2025/8pn2_17768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pn2_17768/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pn2_17768/06_2025/8pn2_17768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pn2_17768/06_2025/8pn2_17768.map" model { file = "/net/cci-nas-00/data/ceres_data/8pn2_17768/06_2025/8pn2_17768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pn2_17768/06_2025/8pn2_17768.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.08, per 1000 atoms: 0.60 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: 4.55 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.35 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: 5.80 Time building geometry restraints manager: 5.40 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: 0.03 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.730 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.027 0.002 TRP E 144 HIS 0.007 0.001 HIS B 421 PHE 0.017 0.001 PHE E 111 TYR 0.020 0.001 TYR F 69 ARG 0.008 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.21547 ( 447) hydrogen bonds : angle 7.88375 ( 1173) covalent geometry : bond 0.00252 (18894) covalent geometry : angle 0.51548 (25674) *********************** 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 : 2.805 Fit side-chains revert: symmetry clash 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: 0.6075 (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: 0.6932 (t70) REVERT: C 122 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8034 (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: 0.6067 (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: 0.7240 (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: 1.2105 time to fit residues: 470.5684 Evaluate side-chains 265 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0000 chunk 177 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.177689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158126 restraints weight = 20124.000| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.74 r_work: 0.3784 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18894 Z= 0.123 Angle : 0.528 5.973 25674 Z= 0.280 Chirality : 0.045 0.146 2856 Planarity : 0.004 0.037 3318 Dihedral : 10.426 88.439 2752 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.88 % Allowed : 9.65 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2334 helix: -0.28 (0.24), residues: 438 sheet: -0.30 (0.22), residues: 432 loop : 0.20 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 144 HIS 0.004 0.001 HIS D 421 PHE 0.021 0.001 PHE C 211 TYR 0.016 0.001 TYR F 69 ARG 0.004 0.001 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 447) hydrogen bonds : angle 5.87908 ( 1173) covalent geometry : bond 0.00282 (18894) covalent geometry : angle 0.52829 (25674) *********************** 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 320 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 1.821 Fit side-chains REVERT: A 111 PHE cc_start: 0.7817 (m-80) cc_final: 0.7576 (m-80) REVERT: A 123 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7661 (mppt) REVERT: A 184 MET cc_start: 0.6723 (ppp) cc_final: 0.6399 (ppp) REVERT: A 377 GLN cc_start: 0.7892 (mt0) cc_final: 0.7546 (mt0) REVERT: A 438 ARG cc_start: 0.7434 (mmt-90) cc_final: 0.7159 (tpp-160) REVERT: A 452 ASP cc_start: 0.7230 (t0) cc_final: 0.6582 (t0) REVERT: B 123 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7574 (mppt) REVERT: B 197 GLU cc_start: 0.7642 (pt0) cc_final: 0.7018 (pm20) REVERT: B 224 ASN cc_start: 0.7015 (m110) cc_final: 0.6153 (t0) REVERT: B 259 TYR cc_start: 0.8034 (t80) cc_final: 0.7112 (t80) REVERT: B 363 ILE cc_start: 0.8096 (mt) cc_final: 0.7731 (mp) REVERT: C 164 ASP cc_start: 0.7256 (m-30) cc_final: 0.6914 (p0) REVERT: C 224 ASN cc_start: 0.7007 (m110) cc_final: 0.6162 (t0) REVERT: C 285 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7671 (mt-10) REVERT: C 320 LYS cc_start: 0.8024 (tttp) cc_final: 0.7620 (ttpt) REVERT: C 325 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6669 (mp-120) REVERT: D 224 ASN cc_start: 0.7074 (m110) cc_final: 0.6181 (t0) REVERT: D 285 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 320 LYS cc_start: 0.7984 (tttp) cc_final: 0.7622 (ttpt) REVERT: D 325 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6638 (mp-120) REVERT: E 224 ASN cc_start: 0.6982 (m110) cc_final: 0.6052 (t0) REVERT: E 259 TYR cc_start: 0.8240 (t80) cc_final: 0.7559 (t80) REVERT: E 452 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6989 (t0) REVERT: F 241 TYR cc_start: 0.8441 (t80) cc_final: 0.7941 (t80) REVERT: F 438 ARG cc_start: 0.7419 (mmt-90) cc_final: 0.7147 (tpp-160) outliers start: 37 outliers final: 18 residues processed: 293 average time/residue: 1.1477 time to fit residues: 383.1444 Evaluate side-chains 262 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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 455 GLN 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 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 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 15 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.170063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149852 restraints weight = 20172.942| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.75 r_work: 0.3695 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18894 Z= 0.256 Angle : 0.639 7.151 25674 Z= 0.338 Chirality : 0.048 0.159 2856 Planarity : 0.005 0.036 3318 Dihedral : 10.305 86.923 2748 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.79 % Allowed : 12.75 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2334 helix: -0.49 (0.24), residues: 438 sheet: -0.61 (0.21), residues: 492 loop : 0.18 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 144 HIS 0.008 0.002 HIS F 248 PHE 0.025 0.002 PHE D 211 TYR 0.020 0.002 TYR A 69 ARG 0.006 0.001 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 447) hydrogen bonds : angle 5.89822 ( 1173) covalent geometry : bond 0.00610 (18894) covalent geometry : angle 0.63927 (25674) *********************** 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 293 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 2.228 Fit side-chains REVERT: A 111 PHE cc_start: 0.7831 (m-80) cc_final: 0.7573 (m-80) REVERT: A 123 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7693 (mppt) REVERT: A 241 TYR cc_start: 0.8624 (t80) cc_final: 0.8102 (t80) REVERT: A 325 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6605 (mp-120) REVERT: A 377 GLN cc_start: 0.8000 (mt0) cc_final: 0.7655 (mt0) REVERT: A 414 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (ttp80) REVERT: A 416 LYS cc_start: 0.8277 (tptm) cc_final: 0.7039 (mptt) REVERT: A 438 ARG cc_start: 0.7393 (mmt-90) cc_final: 0.7140 (tpp-160) REVERT: B 123 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7654 (mppt) REVERT: B 125 ASP cc_start: 0.6737 (p0) cc_final: 0.6100 (m-30) REVERT: B 184 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6509 (mtm) REVERT: B 224 ASN cc_start: 0.7120 (m110) cc_final: 0.6155 (t0) REVERT: B 259 TYR cc_start: 0.8304 (t80) cc_final: 0.7468 (t80) REVERT: B 452 ASP cc_start: 0.7269 (t0) cc_final: 0.7024 (t0) REVERT: C 224 ASN cc_start: 0.7063 (m110) cc_final: 0.6205 (t0) REVERT: C 285 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 299 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7185 (p0) REVERT: C 320 LYS cc_start: 0.8109 (tttp) cc_final: 0.7668 (ttpt) REVERT: D 224 ASN cc_start: 0.7108 (m110) cc_final: 0.6269 (t0) REVERT: D 285 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 320 LYS cc_start: 0.8129 (tttp) cc_final: 0.7678 (ttpt) REVERT: D 363 ILE cc_start: 0.8501 (mt) cc_final: 0.8231 (mt) REVERT: E 123 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7763 (mppt) REVERT: E 184 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6517 (mtm) REVERT: E 224 ASN cc_start: 0.7111 (m110) cc_final: 0.6072 (t0) REVERT: E 416 LYS cc_start: 0.8183 (tptm) cc_final: 0.6890 (mptt) REVERT: F 64 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: F 123 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7738 (mppt) REVERT: F 125 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: F 241 TYR cc_start: 0.8606 (t80) cc_final: 0.7926 (t80) REVERT: F 325 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6676 (mp-120) REVERT: F 414 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7793 (ttp80) REVERT: F 416 LYS cc_start: 0.8303 (tptm) cc_final: 0.7057 (mptt) outliers start: 55 outliers final: 22 residues processed: 260 average time/residue: 1.9009 time to fit residues: 566.6458 Evaluate side-chains 259 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 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 184 MET 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 299 ASP 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 367 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR 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 254 LEU 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 414 ARG 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 11 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN F 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150208 restraints weight = 20292.029| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.65 r_work: 0.3693 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18894 Z= 0.231 Angle : 0.615 7.118 25674 Z= 0.325 Chirality : 0.047 0.153 2856 Planarity : 0.004 0.032 3318 Dihedral : 10.031 87.637 2748 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.66 % Allowed : 13.72 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2334 helix: -0.50 (0.24), residues: 438 sheet: -0.82 (0.22), residues: 480 loop : 0.09 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 144 HIS 0.007 0.001 HIS A 248 PHE 0.022 0.002 PHE D 211 TYR 0.015 0.002 TYR D 259 ARG 0.006 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 447) hydrogen bonds : angle 5.86691 ( 1173) covalent geometry : bond 0.00549 (18894) covalent geometry : angle 0.61547 (25674) *********************** 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 318 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 2.270 Fit side-chains REVERT: A 111 PHE cc_start: 0.7764 (m-80) cc_final: 0.7508 (m-80) REVERT: A 123 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7606 (mppt) REVERT: A 241 TYR cc_start: 0.8642 (t80) cc_final: 0.7889 (t80) REVERT: A 363 ILE cc_start: 0.8336 (mt) cc_final: 0.8115 (mt) REVERT: A 414 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7662 (tpp80) REVERT: A 416 LYS cc_start: 0.8312 (tptm) cc_final: 0.6887 (mptt) REVERT: A 438 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.7009 (tpp-160) REVERT: A 452 ASP cc_start: 0.7202 (t0) cc_final: 0.6848 (t0) REVERT: B 64 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6365 (pp20) REVERT: B 123 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7599 (mppt) REVERT: B 125 ASP cc_start: 0.6684 (p0) cc_final: 0.5990 (m-30) REVERT: B 184 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6448 (mtm) REVERT: B 224 ASN cc_start: 0.7098 (m110) cc_final: 0.6037 (t0) REVERT: B 259 TYR cc_start: 0.8297 (t80) cc_final: 0.7469 (t80) REVERT: B 264 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7786 (pp20) REVERT: B 265 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8522 (ptp-170) REVERT: B 341 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7790 (ptm160) REVERT: C 224 ASN cc_start: 0.7015 (m110) cc_final: 0.6064 (t0) REVERT: C 299 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7113 (p0) REVERT: C 320 LYS cc_start: 0.8093 (tttp) cc_final: 0.7623 (ttpt) REVERT: C 416 LYS cc_start: 0.8296 (tptm) cc_final: 0.7027 (mptt) REVERT: C 456 GLN cc_start: 0.6783 (tp40) cc_final: 0.6447 (mm110) REVERT: D 190 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: D 224 ASN cc_start: 0.7140 (m110) cc_final: 0.6156 (t0) REVERT: D 241 TYR cc_start: 0.8559 (t80) cc_final: 0.8309 (t80) REVERT: D 285 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 320 LYS cc_start: 0.8091 (tttp) cc_final: 0.7589 (ttpt) REVERT: D 363 ILE cc_start: 0.8588 (mt) cc_final: 0.8348 (mt) REVERT: E 64 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6384 (pp20) REVERT: E 123 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7693 (mppt) REVERT: E 184 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6480 (mtm) REVERT: E 224 ASN cc_start: 0.7075 (m110) cc_final: 0.5942 (t0) REVERT: E 265 ARG cc_start: 0.8677 (ptm160) cc_final: 0.8441 (ptp-170) REVERT: E 416 LYS cc_start: 0.8180 (tptm) cc_final: 0.6746 (mptt) REVERT: F 64 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5942 (pp20) REVERT: F 123 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7681 (mppt) REVERT: F 125 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: F 241 TYR cc_start: 0.8632 (t80) cc_final: 0.8076 (t80) REVERT: F 414 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7673 (tpp80) REVERT: F 416 LYS cc_start: 0.8313 (tptm) cc_final: 0.6932 (mptt) outliers start: 72 outliers final: 38 residues processed: 281 average time/residue: 1.1939 time to fit residues: 382.0512 Evaluate side-chains 278 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP 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 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 184 MET 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 265 ARG Chi-restraints excluded: chain B residue 341 ARG 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 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 190 ASP 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 111 PHE Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 313 VAL 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 303 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 378 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 ARG 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 25 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 222 optimal weight: 0.0270 chunk 221 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 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 = 0.4025 r_free = 0.4025 target = 0.175219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155742 restraints weight = 20263.882| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.72 r_work: 0.3758 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18894 Z= 0.116 Angle : 0.520 6.158 25674 Z= 0.274 Chirality : 0.043 0.139 2856 Planarity : 0.003 0.041 3318 Dihedral : 8.599 80.606 2748 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.05 % Allowed : 14.84 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2334 helix: -0.10 (0.25), residues: 438 sheet: -0.74 (0.23), residues: 444 loop : 0.14 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 144 HIS 0.002 0.000 HIS D 248 PHE 0.025 0.001 PHE D 211 TYR 0.014 0.001 TYR D 259 ARG 0.005 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 447) hydrogen bonds : angle 5.47915 ( 1173) covalent geometry : bond 0.00275 (18894) covalent geometry : angle 0.52025 (25674) *********************** 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 319 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 1.891 Fit side-chains REVERT: A 111 PHE cc_start: 0.7906 (m-80) cc_final: 0.7701 (m-80) REVERT: A 123 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7722 (mppt) REVERT: A 184 MET cc_start: 0.6833 (ppp) cc_final: 0.6541 (ppp) REVERT: A 224 ASN cc_start: 0.7254 (m110) cc_final: 0.6301 (t0) REVERT: A 241 TYR cc_start: 0.8601 (t80) cc_final: 0.8072 (t80) REVERT: A 416 LYS cc_start: 0.8238 (tptm) cc_final: 0.6972 (mptt) REVERT: A 452 ASP cc_start: 0.7217 (t0) cc_final: 0.7006 (t0) REVERT: B 64 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6456 (pp20) REVERT: B 123 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7618 (mppt) REVERT: B 125 ASP cc_start: 0.6732 (p0) cc_final: 0.6147 (m-30) REVERT: B 184 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6499 (mtm) REVERT: B 224 ASN cc_start: 0.7027 (m110) cc_final: 0.6153 (t0) REVERT: B 259 TYR cc_start: 0.8190 (t80) cc_final: 0.7140 (t80) REVERT: B 363 ILE cc_start: 0.8156 (mt) cc_final: 0.7839 (mp) REVERT: C 224 ASN cc_start: 0.7040 (m110) cc_final: 0.6090 (t0) REVERT: C 285 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 299 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7156 (p0) REVERT: C 320 LYS cc_start: 0.8057 (tttp) cc_final: 0.7668 (ttpt) REVERT: C 325 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6920 (mm110) REVERT: C 416 LYS cc_start: 0.8280 (tptm) cc_final: 0.7157 (mptt) REVERT: C 456 GLN cc_start: 0.6808 (tp40) cc_final: 0.6485 (mm110) REVERT: D 125 ASP cc_start: 0.6734 (t0) cc_final: 0.6266 (p0) REVERT: D 224 ASN cc_start: 0.7084 (m110) cc_final: 0.6193 (t0) REVERT: D 285 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7736 (mt-10) REVERT: D 320 LYS cc_start: 0.8066 (tttp) cc_final: 0.7700 (ttpt) REVERT: D 325 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6988 (mm110) REVERT: D 363 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (mt) REVERT: D 452 ASP cc_start: 0.7244 (t0) cc_final: 0.6879 (t0) REVERT: D 456 GLN cc_start: 0.6947 (tp40) cc_final: 0.6616 (mm110) REVERT: E 64 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: E 224 ASN cc_start: 0.7026 (m110) cc_final: 0.6074 (t0) REVERT: E 363 ILE cc_start: 0.8284 (mt) cc_final: 0.7968 (mp) REVERT: E 416 LYS cc_start: 0.8062 (tptm) cc_final: 0.6883 (mptt) REVERT: E 452 ASP cc_start: 0.7151 (t0) cc_final: 0.6858 (t0) REVERT: F 64 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: F 123 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7688 (mppt) REVERT: F 125 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: F 224 ASN cc_start: 0.7240 (m110) cc_final: 0.6353 (t0) REVERT: F 416 LYS cc_start: 0.8268 (tptm) cc_final: 0.7008 (mptt) outliers start: 60 outliers final: 29 residues processed: 291 average time/residue: 1.0832 time to fit residues: 361.4347 Evaluate side-chains 274 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE 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 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 184 MET 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 404 ILE 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 211 PHE Chi-restraints excluded: chain D residue 264 GLU 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 E residue 64 GLU Chi-restraints excluded: chain E residue 111 PHE 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 111 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 200 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 62 optimal weight: 0.0040 chunk 193 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 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 = 0.4035 r_free = 0.4035 target = 0.176181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156599 restraints weight = 20270.742| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.74 r_work: 0.3766 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18894 Z= 0.115 Angle : 0.515 6.074 25674 Z= 0.272 Chirality : 0.043 0.135 2856 Planarity : 0.003 0.043 3318 Dihedral : 7.883 61.639 2748 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.15 % Allowed : 16.16 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2334 helix: -0.04 (0.25), residues: 438 sheet: -0.70 (0.23), residues: 444 loop : 0.19 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 275 HIS 0.002 0.000 HIS F 141 PHE 0.026 0.001 PHE D 211 TYR 0.023 0.001 TYR A 69 ARG 0.007 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 447) hydrogen bonds : angle 5.37722 ( 1173) covalent geometry : bond 0.00271 (18894) covalent geometry : angle 0.51454 (25674) *********************** 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 322 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 2.076 Fit side-chains REVERT: A 64 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6105 (tt0) REVERT: A 123 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7681 (mppt) REVERT: A 125 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: A 184 MET cc_start: 0.6730 (ppp) cc_final: 0.6388 (ppp) REVERT: A 224 ASN cc_start: 0.7228 (m110) cc_final: 0.6246 (t0) REVERT: A 414 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7696 (tpp80) REVERT: A 416 LYS cc_start: 0.8220 (tptm) cc_final: 0.6959 (mptt) REVERT: B 64 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: B 123 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7542 (mppt) REVERT: B 125 ASP cc_start: 0.6810 (p0) cc_final: 0.6190 (m-30) REVERT: B 184 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6481 (mtm) REVERT: B 224 ASN cc_start: 0.6946 (m110) cc_final: 0.6049 (t0) REVERT: B 259 TYR cc_start: 0.8174 (t80) cc_final: 0.7276 (t80) REVERT: B 265 ARG cc_start: 0.8692 (ptm160) cc_final: 0.8448 (ptp-170) REVERT: B 363 ILE cc_start: 0.8138 (mt) cc_final: 0.7731 (mp) REVERT: B 416 LYS cc_start: 0.8084 (tptm) cc_final: 0.6815 (mptt) REVERT: C 224 ASN cc_start: 0.6975 (m110) cc_final: 0.6037 (t0) REVERT: C 285 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 299 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7205 (p0) REVERT: C 320 LYS cc_start: 0.8018 (tttp) cc_final: 0.7634 (ttpt) REVERT: C 325 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6853 (mm110) REVERT: C 416 LYS cc_start: 0.8291 (tptm) cc_final: 0.7139 (mptt) REVERT: C 452 ASP cc_start: 0.7195 (t0) cc_final: 0.6890 (t0) REVERT: C 456 GLN cc_start: 0.6894 (tp40) cc_final: 0.6583 (mm110) REVERT: D 224 ASN cc_start: 0.7067 (m110) cc_final: 0.6183 (t0) REVERT: D 285 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7717 (mt-10) REVERT: D 320 LYS cc_start: 0.7993 (tttp) cc_final: 0.7644 (ttpt) REVERT: D 325 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6935 (mm110) REVERT: D 456 GLN cc_start: 0.6880 (tp40) cc_final: 0.6545 (mm110) REVERT: E 64 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: E 125 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: E 224 ASN cc_start: 0.6993 (m110) cc_final: 0.6028 (t0) REVERT: E 363 ILE cc_start: 0.8213 (mt) cc_final: 0.7856 (mp) REVERT: E 416 LYS cc_start: 0.8037 (tptm) cc_final: 0.6877 (mptt) REVERT: E 452 ASP cc_start: 0.7078 (t0) cc_final: 0.6832 (t0) REVERT: F 64 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6112 (tt0) REVERT: F 125 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: F 224 ASN cc_start: 0.7240 (m110) cc_final: 0.6309 (t0) REVERT: F 241 TYR cc_start: 0.8535 (t80) cc_final: 0.8060 (t80) REVERT: F 416 LYS cc_start: 0.8246 (tptm) cc_final: 0.6990 (mptt) outliers start: 62 outliers final: 29 residues processed: 295 average time/residue: 1.1273 time to fit residues: 379.1491 Evaluate side-chains 284 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU 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 184 MET 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 404 ILE 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 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 404 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 111 PHE 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 F residue 64 GLU Chi-restraints excluded: chain F residue 111 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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 = 0.3979 r_free = 0.3979 target = 0.173028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152284 restraints weight = 20040.437| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.85 r_work: 0.3693 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1910 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= 0.130 Angle : 0.525 6.157 25674 Z= 0.278 Chirality : 0.043 0.132 2856 Planarity : 0.003 0.032 3318 Dihedral : 7.628 56.373 2748 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.30 % Allowed : 16.51 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2334 helix: -0.01 (0.25), residues: 438 sheet: -0.72 (0.23), residues: 444 loop : 0.18 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 275 HIS 0.002 0.001 HIS A 248 PHE 0.026 0.001 PHE D 211 TYR 0.013 0.001 TYR D 259 ARG 0.007 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 447) hydrogen bonds : angle 5.38248 ( 1173) covalent geometry : bond 0.00309 (18894) covalent geometry : angle 0.52488 (25674) *********************** 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 310 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 1.925 Fit side-chains REVERT: A 64 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6024 (tt0) REVERT: A 123 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7677 (mppt) REVERT: A 224 ASN cc_start: 0.7239 (m110) cc_final: 0.6249 (t0) REVERT: A 241 TYR cc_start: 0.8598 (t80) cc_final: 0.8147 (t80) REVERT: A 325 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6671 (mp-120) REVERT: A 414 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7672 (tpp80) REVERT: A 416 LYS cc_start: 0.8286 (tptm) cc_final: 0.7015 (mptt) REVERT: A 438 ARG cc_start: 0.7357 (mmt-90) cc_final: 0.7116 (tpp-160) REVERT: B 64 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: B 123 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7601 (mppt) REVERT: B 125 ASP cc_start: 0.6876 (p0) cc_final: 0.6268 (m-30) REVERT: B 184 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6507 (mtm) REVERT: B 224 ASN cc_start: 0.7001 (m110) cc_final: 0.6017 (t0) REVERT: B 259 TYR cc_start: 0.8267 (t80) cc_final: 0.7164 (t80) REVERT: B 264 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: B 265 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8473 (ptp-170) REVERT: B 416 LYS cc_start: 0.8152 (tptm) cc_final: 0.6898 (mptt) REVERT: C 224 ASN cc_start: 0.6924 (m110) cc_final: 0.5941 (t0) REVERT: C 299 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7218 (p0) REVERT: C 320 LYS cc_start: 0.8032 (tttp) cc_final: 0.7635 (ttpt) REVERT: C 325 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6976 (mm110) REVERT: C 416 LYS cc_start: 0.8345 (tptm) cc_final: 0.7152 (mptt) REVERT: C 452 ASP cc_start: 0.7189 (t0) cc_final: 0.6951 (t0) REVERT: C 456 GLN cc_start: 0.6880 (tp40) cc_final: 0.6558 (mm110) REVERT: D 224 ASN cc_start: 0.7045 (m110) cc_final: 0.6161 (t0) REVERT: D 285 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 299 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7198 (p0) REVERT: D 320 LYS cc_start: 0.8067 (tttp) cc_final: 0.7661 (ttpt) REVERT: D 325 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7009 (mm110) REVERT: D 456 GLN cc_start: 0.6902 (tp40) cc_final: 0.6560 (mm110) REVERT: E 64 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: E 125 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: E 220 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7699 (mtp85) REVERT: E 224 ASN cc_start: 0.6989 (m110) cc_final: 0.5953 (t0) REVERT: E 416 LYS cc_start: 0.8123 (tptm) cc_final: 0.6936 (mptt) REVERT: F 64 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6038 (tt0) REVERT: F 125 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6504 (m-30) REVERT: F 325 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6672 (mp-120) REVERT: F 414 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7750 (tpp80) REVERT: F 416 LYS cc_start: 0.8308 (tptm) cc_final: 0.7067 (mptt) outliers start: 65 outliers final: 38 residues processed: 286 average time/residue: 1.2047 time to fit residues: 393.8713 Evaluate side-chains 295 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 325 GLN 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 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 184 MET 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 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 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 111 PHE 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 111 PHE 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 325 GLN 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 414 ARG 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 121 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 213 optimal weight: 0.0970 chunk 31 optimal weight: 0.0040 chunk 154 optimal weight: 1.9990 chunk 174 optimal weight: 0.0020 chunk 187 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN 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 = 0.3983 r_free = 0.3983 target = 0.173463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152828 restraints weight = 19993.067| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.86 r_work: 0.3708 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18894 Z= 0.122 Angle : 0.520 6.080 25674 Z= 0.275 Chirality : 0.043 0.132 2856 Planarity : 0.003 0.033 3318 Dihedral : 7.439 55.197 2748 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.74 % Allowed : 17.07 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2334 helix: 0.02 (0.25), residues: 438 sheet: -0.69 (0.23), residues: 444 loop : 0.18 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 275 HIS 0.002 0.001 HIS A 248 PHE 0.027 0.001 PHE D 211 TYR 0.013 0.001 TYR D 259 ARG 0.007 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 447) hydrogen bonds : angle 5.34876 ( 1173) covalent geometry : bond 0.00287 (18894) covalent geometry : angle 0.52049 (25674) *********************** 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 315 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 2.135 Fit side-chains REVERT: A 64 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6013 (tt0) REVERT: A 123 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7669 (mppt) REVERT: A 125 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6529 (m-30) REVERT: A 184 MET cc_start: 0.6861 (ppp) cc_final: 0.6444 (ppp) REVERT: A 224 ASN cc_start: 0.7242 (m110) cc_final: 0.6250 (t0) REVERT: A 414 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7674 (tpp80) REVERT: A 416 LYS cc_start: 0.8258 (tptm) cc_final: 0.7021 (mptt) REVERT: A 438 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.7117 (tpp-160) REVERT: B 64 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: B 123 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7582 (mppt) REVERT: B 125 ASP cc_start: 0.6867 (p0) cc_final: 0.6260 (m-30) REVERT: B 224 ASN cc_start: 0.7002 (m110) cc_final: 0.6008 (t0) REVERT: B 259 TYR cc_start: 0.8232 (t80) cc_final: 0.7193 (t80) REVERT: B 264 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: B 265 ARG cc_start: 0.8692 (ptm160) cc_final: 0.8463 (ptp-170) REVERT: B 416 LYS cc_start: 0.8125 (tptm) cc_final: 0.6893 (mptt) REVERT: C 89 GLN cc_start: 0.6309 (tp40) cc_final: 0.6016 (tt0) REVERT: C 224 ASN cc_start: 0.6943 (m110) cc_final: 0.5938 (t0) REVERT: C 299 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7186 (p0) REVERT: C 320 LYS cc_start: 0.8010 (tttp) cc_final: 0.7628 (ttpt) REVERT: C 325 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6979 (mm110) REVERT: C 416 LYS cc_start: 0.8346 (tptm) cc_final: 0.7141 (mptt) REVERT: C 452 ASP cc_start: 0.7173 (t0) cc_final: 0.6953 (t0) REVERT: C 456 GLN cc_start: 0.6883 (tp40) cc_final: 0.6561 (mm110) REVERT: D 224 ASN cc_start: 0.7043 (m110) cc_final: 0.6173 (t0) REVERT: D 285 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 299 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7226 (p0) REVERT: D 320 LYS cc_start: 0.8044 (tttp) cc_final: 0.7651 (ttpt) REVERT: D 325 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7018 (mm110) REVERT: D 456 GLN cc_start: 0.6882 (tp40) cc_final: 0.6540 (mm110) REVERT: E 64 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: E 125 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6426 (m-30) REVERT: E 220 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7657 (mtp85) REVERT: E 224 ASN cc_start: 0.6979 (m110) cc_final: 0.5961 (t0) REVERT: E 259 TYR cc_start: 0.8358 (t80) cc_final: 0.7746 (t80) REVERT: E 416 LYS cc_start: 0.8136 (tptm) cc_final: 0.6938 (mptt) REVERT: F 64 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6029 (tt0) REVERT: F 125 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: F 224 ASN cc_start: 0.7224 (m110) cc_final: 0.6272 (t0) REVERT: F 241 TYR cc_start: 0.8449 (t80) cc_final: 0.7837 (t80) REVERT: F 414 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7721 (tpp80) REVERT: F 416 LYS cc_start: 0.8299 (tptm) cc_final: 0.7053 (mptt) outliers start: 54 outliers final: 35 residues processed: 297 average time/residue: 1.1299 time to fit residues: 382.6240 Evaluate side-chains 294 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU 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 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 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 111 PHE 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 111 PHE 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 414 ARG 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 17 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151821 restraints weight = 20050.217| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.86 r_work: 0.3718 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1963 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= 0.142 Angle : 0.540 6.693 25674 Z= 0.286 Chirality : 0.044 0.133 2856 Planarity : 0.003 0.031 3318 Dihedral : 7.505 55.966 2748 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.95 % Allowed : 17.28 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2334 helix: -0.05 (0.25), residues: 438 sheet: -0.59 (0.23), residues: 438 loop : 0.14 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 275 HIS 0.003 0.001 HIS A 248 PHE 0.026 0.002 PHE D 211 TYR 0.015 0.001 TYR C 241 ARG 0.008 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 447) hydrogen bonds : angle 5.41594 ( 1173) covalent geometry : bond 0.00338 (18894) covalent geometry : angle 0.53984 (25674) *********************** 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 307 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 1.934 Fit side-chains REVERT: A 64 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5963 (tt0) REVERT: A 123 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7657 (mppt) REVERT: A 125 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: A 184 MET cc_start: 0.6830 (ppp) cc_final: 0.6463 (ppp) REVERT: A 224 ASN cc_start: 0.7265 (m110) cc_final: 0.6275 (t0) REVERT: A 241 TYR cc_start: 0.8556 (t80) cc_final: 0.7991 (t80) REVERT: A 414 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7692 (tpp80) REVERT: A 416 LYS cc_start: 0.8306 (tptm) cc_final: 0.7034 (mptt) REVERT: A 438 ARG cc_start: 0.7363 (mmt-90) cc_final: 0.7111 (tpp-160) REVERT: B 64 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: B 123 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7577 (mppt) REVERT: B 125 ASP cc_start: 0.6895 (p0) cc_final: 0.6289 (m-30) REVERT: B 224 ASN cc_start: 0.7005 (m110) cc_final: 0.5971 (t0) REVERT: B 259 TYR cc_start: 0.8264 (t80) cc_final: 0.7229 (t80) REVERT: B 264 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: B 265 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8483 (ptp-170) REVERT: B 416 LYS cc_start: 0.8085 (tptm) cc_final: 0.6832 (mptt) REVERT: C 89 GLN cc_start: 0.6317 (tp40) cc_final: 0.6011 (tt0) REVERT: C 224 ASN cc_start: 0.6985 (m110) cc_final: 0.5931 (t0) REVERT: C 299 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7190 (p0) REVERT: C 320 LYS cc_start: 0.8026 (tttp) cc_final: 0.7623 (ttpt) REVERT: C 416 LYS cc_start: 0.8260 (tptm) cc_final: 0.7061 (mptt) REVERT: C 452 ASP cc_start: 0.7172 (t0) cc_final: 0.6957 (t0) REVERT: C 456 GLN cc_start: 0.6874 (tp40) cc_final: 0.6545 (mm110) REVERT: D 224 ASN cc_start: 0.7125 (m110) cc_final: 0.6151 (t0) REVERT: D 285 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 299 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7245 (p0) REVERT: D 320 LYS cc_start: 0.8065 (tttp) cc_final: 0.7649 (ttpt) REVERT: D 325 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7061 (mm110) REVERT: D 456 GLN cc_start: 0.6908 (tp40) cc_final: 0.6562 (mm110) REVERT: E 64 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: E 125 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6474 (m-30) REVERT: E 224 ASN cc_start: 0.7020 (m110) cc_final: 0.6012 (t0) REVERT: E 416 LYS cc_start: 0.8154 (tptm) cc_final: 0.6928 (mptt) REVERT: F 64 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5995 (tt0) REVERT: F 125 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6510 (m-30) REVERT: F 224 ASN cc_start: 0.7189 (m110) cc_final: 0.6228 (t0) REVERT: F 241 TYR cc_start: 0.8471 (t80) cc_final: 0.7868 (t80) REVERT: F 414 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7724 (tpp80) REVERT: F 416 LYS cc_start: 0.8294 (tptm) cc_final: 0.7048 (mptt) outliers start: 58 outliers final: 36 residues processed: 285 average time/residue: 1.1980 time to fit residues: 387.5444 Evaluate side-chains 291 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 273 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 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 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 D residue 418 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 111 PHE 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 414 ARG 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 73 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 170 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151076 restraints weight = 20085.019| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.86 r_work: 0.3682 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1981 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= 0.159 Angle : 0.563 6.881 25674 Z= 0.299 Chirality : 0.045 0.133 2856 Planarity : 0.004 0.078 3318 Dihedral : 7.621 57.577 2748 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.54 % Allowed : 17.84 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2334 helix: -0.09 (0.25), residues: 438 sheet: -0.57 (0.23), residues: 438 loop : 0.11 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 275 HIS 0.004 0.001 HIS D 248 PHE 0.026 0.002 PHE D 211 TYR 0.016 0.001 TYR C 241 ARG 0.015 0.001 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 447) hydrogen bonds : angle 5.47770 ( 1173) covalent geometry : bond 0.00379 (18894) covalent geometry : angle 0.56258 (25674) ********************** 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 286 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 2.080 Fit side-chains REVERT: A 64 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: A 123 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7655 (mppt) REVERT: A 184 MET cc_start: 0.6850 (ppp) cc_final: 0.6475 (ppp) REVERT: A 224 ASN cc_start: 0.7274 (m110) cc_final: 0.6308 (t0) REVERT: A 241 TYR cc_start: 0.8630 (t80) cc_final: 0.7992 (t80) REVERT: A 414 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7745 (tpp80) REVERT: A 416 LYS cc_start: 0.8313 (tptm) cc_final: 0.7035 (mptt) REVERT: B 64 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: B 123 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7583 (mppt) REVERT: B 125 ASP cc_start: 0.6921 (p0) cc_final: 0.6333 (m-30) REVERT: B 224 ASN cc_start: 0.7020 (m110) cc_final: 0.5984 (t0) REVERT: B 259 TYR cc_start: 0.8296 (t80) cc_final: 0.7269 (t80) REVERT: B 264 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: B 265 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8490 (ptp-170) REVERT: B 416 LYS cc_start: 0.8018 (tptm) cc_final: 0.6773 (mptt) REVERT: C 89 GLN cc_start: 0.6321 (tp40) cc_final: 0.5932 (tt0) REVERT: C 224 ASN cc_start: 0.7001 (m110) cc_final: 0.5938 (t0) REVERT: C 299 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7152 (p0) REVERT: C 320 LYS cc_start: 0.8069 (tttp) cc_final: 0.7656 (ttpt) REVERT: C 416 LYS cc_start: 0.8318 (tptm) cc_final: 0.7118 (mptt) REVERT: C 452 ASP cc_start: 0.7198 (t0) cc_final: 0.6985 (t0) REVERT: C 456 GLN cc_start: 0.6875 (tp40) cc_final: 0.6537 (mm110) REVERT: D 224 ASN cc_start: 0.7126 (m110) cc_final: 0.6136 (t0) REVERT: D 285 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7628 (mt-10) REVERT: D 299 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7251 (p0) REVERT: D 320 LYS cc_start: 0.8097 (tttp) cc_final: 0.7678 (ttpt) REVERT: D 325 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7098 (mm110) REVERT: D 456 GLN cc_start: 0.6912 (tp40) cc_final: 0.6552 (mm110) REVERT: E 64 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: E 125 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: E 224 ASN cc_start: 0.7072 (m110) cc_final: 0.6037 (t0) REVERT: E 416 LYS cc_start: 0.8194 (tptm) cc_final: 0.6943 (mptt) REVERT: F 64 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5992 (tt0) REVERT: F 184 MET cc_start: 0.6669 (mtm) cc_final: 0.6193 (ptt) REVERT: F 224 ASN cc_start: 0.7204 (m110) cc_final: 0.6236 (t0) REVERT: F 241 TYR cc_start: 0.8461 (t80) cc_final: 0.7935 (t80) REVERT: F 414 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7753 (tpp80) REVERT: F 416 LYS cc_start: 0.8330 (tptm) cc_final: 0.7081 (mptt) outliers start: 50 outliers final: 35 residues processed: 270 average time/residue: 1.1741 time to fit residues: 360.3972 Evaluate side-chains 276 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 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 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP 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 111 PHE 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 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 414 ARG 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 109 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151994 restraints weight = 19993.839| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.86 r_work: 0.3737 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2002 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= 0.141 Angle : 0.552 6.648 25674 Z= 0.293 Chirality : 0.044 0.132 2856 Planarity : 0.003 0.036 3318 Dihedral : 7.476 56.882 2748 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.39 % Allowed : 18.29 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2334 helix: -0.07 (0.25), residues: 438 sheet: -0.56 (0.23), residues: 438 loop : 0.13 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 275 HIS 0.003 0.001 HIS D 248 PHE 0.027 0.002 PHE D 211 TYR 0.014 0.001 TYR D 259 ARG 0.007 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 447) hydrogen bonds : angle 5.44533 ( 1173) covalent geometry : bond 0.00337 (18894) covalent geometry : angle 0.55170 (25674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13644.77 seconds wall clock time: 237 minutes 28.45 seconds (14248.45 seconds total)