Starting phenix.real_space_refine on Mon Aug 25 21:00:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2025/8u7q_41989.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18992 2.51 5 N 5192 2.21 5 O 6056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "E" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "F" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "G" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 7.04, per 1000 atoms: 0.23 Number of scatterers: 30520 At special positions: 0 Unit cell: (151.96, 151.96, 112.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 6056 8.00 N 5192 7.00 C 18992 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 48 sheets defined 40.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.136A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.322A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.319A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.166A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 84 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.139A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.297A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 84 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.138A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 84 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 256 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.341A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.678A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER A 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.626A pdb=" N SER D 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER B 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.566A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.632A pdb=" N SER C 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU E 209 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE E 221 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER E 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 509 through 510 removed outlier: 3.616A pdb=" N SER H 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER F 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER G 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9523 1.34 - 1.45: 3862 1.45 - 1.57: 17231 1.57 - 1.69: 152 1.69 - 1.81: 312 Bond restraints: 31080 Sorted by residual: bond pdb=" N VAL C 350 " pdb=" CA VAL C 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.85e+01 bond pdb=" N VAL B 350 " pdb=" CA VAL B 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.83e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.53e+01 bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 31075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 41300 3.13 - 6.26: 775 6.26 - 9.39: 143 9.39 - 12.52: 54 12.52 - 15.65: 16 Bond angle restraints: 42288 Sorted by residual: angle pdb=" PA ATP H 604 " pdb=" O3A ATP H 604 " pdb=" PB ATP H 604 " ideal model delta sigma weight residual 136.83 121.18 15.65 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 121.23 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP G 604 " pdb=" O3A ATP G 604 " pdb=" PB ATP G 604 " ideal model delta sigma weight residual 136.83 121.25 15.58 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.30e+02 ... (remaining 42283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 17840 33.95 - 67.89: 911 67.89 - 101.84: 169 101.84 - 135.79: 6 135.79 - 169.73: 26 Dihedral angle restraints: 18952 sinusoidal: 8008 harmonic: 10944 Sorted by residual: dihedral pdb=" O3B GTP F 601 " pdb=" O3A GTP F 601 " pdb=" PB GTP F 601 " pdb=" PA GTP F 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.81 -169.73 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PB GTP G 601 " pdb=" PA GTP G 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.59 -169.51 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.17 163.76 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 18949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4308 0.077 - 0.154: 476 0.154 - 0.231: 37 0.231 - 0.308: 15 0.308 - 0.385: 60 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA PHE B 24 " pdb=" N PHE B 24 " pdb=" C PHE B 24 " pdb=" CB PHE B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA PHE H 24 " pdb=" N PHE H 24 " pdb=" C PHE H 24 " pdb=" CB PHE H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4893 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO D 123 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 122 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO C 123 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 122 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 123 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.041 5.00e-02 4.00e+02 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10241 2.84 - 3.36: 29431 3.36 - 3.87: 49355 3.87 - 4.39: 60214 4.39 - 4.90: 104744 Nonbonded interactions: 253985 Sorted by model distance: nonbonded pdb=" O ASP E 170 " pdb=" OG1 THR E 173 " model vdw 2.325 3.040 nonbonded pdb=" O ASP G 170 " pdb=" OG1 THR G 173 " model vdw 2.326 3.040 nonbonded pdb=" O ASP F 170 " pdb=" OG1 THR F 173 " model vdw 2.326 3.040 nonbonded pdb=" O ASP H 170 " pdb=" OG1 THR H 173 " model vdw 2.326 3.040 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.345 3.040 ... (remaining 253980 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.350 Find NCS groups from input model: 0.940 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31080 Z= 0.283 Angle : 1.092 15.647 42288 Z= 0.583 Chirality : 0.063 0.385 4896 Planarity : 0.005 0.073 5208 Dihedral : 20.740 169.733 11976 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 0.73 % Allowed : 15.98 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.14), residues: 3840 helix: -0.24 (0.14), residues: 1392 sheet: -1.25 (0.26), residues: 368 loop : -0.31 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.010 0.001 TYR G 348 PHE 0.008 0.001 PHE G 41 HIS 0.004 0.001 HIS D 507 Details of bonding type rmsd covalent geometry : bond 0.00563 (31080) covalent geometry : angle 1.09187 (42288) hydrogen bonds : bond 0.15891 ( 1168) hydrogen bonds : angle 6.94131 ( 3222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 399 average time/residue: 0.1905 time to fit residues: 122.9722 Evaluate side-chains 347 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN B 368 GLN C 368 GLN D 368 GLN E 94 ASN E 368 GLN E 498 GLN F 94 ASN F 368 GLN G 94 ASN G 368 GLN H 94 ASN H 368 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138866 restraints weight = 34253.657| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.13 r_work: 0.3151 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31080 Z= 0.139 Angle : 0.637 5.890 42288 Z= 0.318 Chirality : 0.046 0.170 4896 Planarity : 0.004 0.050 5208 Dihedral : 17.730 149.846 5138 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 2.18 % Allowed : 17.44 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.14), residues: 3840 helix: 0.32 (0.14), residues: 1416 sheet: -1.77 (0.24), residues: 424 loop : 0.06 (0.15), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 253 TYR 0.007 0.001 TYR E 282 PHE 0.008 0.001 PHE G 35 HIS 0.004 0.001 HIS C 507 Details of bonding type rmsd covalent geometry : bond 0.00333 (31080) covalent geometry : angle 0.63709 (42288) hydrogen bonds : bond 0.03439 ( 1168) hydrogen bonds : angle 5.18368 ( 3222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 412 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 MET cc_start: 0.7725 (mpp) cc_final: 0.7454 (ptp) outliers start: 69 outliers final: 46 residues processed: 443 average time/residue: 0.1682 time to fit residues: 123.6935 Evaluate side-chains 374 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 31 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 112 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN A 171 HIS A 230 ASN A 303 ASN A 368 GLN B 94 ASN B 112 GLN B 171 HIS B 230 ASN B 303 ASN B 368 GLN C 94 ASN C 112 GLN C 171 HIS C 230 ASN C 303 ASN C 368 GLN D 94 ASN D 112 GLN D 171 HIS D 230 ASN D 303 ASN D 368 GLN E 112 GLN E 230 ASN E 303 ASN E 368 GLN F 171 HIS F 230 ASN F 303 ASN F 368 GLN G 171 HIS G 230 ASN G 303 ASN G 368 GLN H 112 GLN H 171 HIS H 230 ASN H 303 ASN H 368 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139027 restraints weight = 34069.347| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.13 r_work: 0.3498 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31080 Z= 0.120 Angle : 0.575 6.413 42288 Z= 0.289 Chirality : 0.043 0.139 4896 Planarity : 0.004 0.039 5208 Dihedral : 15.927 148.160 5136 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 4.02 % Allowed : 17.94 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3840 helix: 0.53 (0.14), residues: 1432 sheet: -1.77 (0.26), residues: 344 loop : 0.22 (0.15), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 412 TYR 0.008 0.001 TYR B 411 PHE 0.007 0.001 PHE F 35 HIS 0.005 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00282 (31080) covalent geometry : angle 0.57470 (42288) hydrogen bonds : bond 0.03080 ( 1168) hydrogen bonds : angle 4.81355 ( 3222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 340 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7039 (mt0) REVERT: A 337 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7403 (ptp) REVERT: B 112 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7029 (mt0) REVERT: B 337 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7403 (ptp) REVERT: C 112 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7051 (mt0) REVERT: C 337 MET cc_start: 0.7849 (mpp) cc_final: 0.7431 (ptp) REVERT: D 112 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: D 337 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (ptp) REVERT: E 112 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: G 337 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7384 (ptp) REVERT: H 112 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: H 337 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7399 (ptp) outliers start: 127 outliers final: 61 residues processed: 419 average time/residue: 0.1548 time to fit residues: 109.6731 Evaluate side-chains 380 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 287 optimal weight: 3.9990 chunk 369 optimal weight: 0.0270 chunk 314 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 318 optimal weight: 2.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 507 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 507 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 507 HIS E 112 GLN E 171 HIS E 303 ASN E 507 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 507 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS H 112 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131713 restraints weight = 34246.374| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.17 r_work: 0.3386 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31080 Z= 0.178 Angle : 0.618 6.884 42288 Z= 0.311 Chirality : 0.046 0.156 4896 Planarity : 0.004 0.035 5208 Dihedral : 15.871 145.487 5136 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.11 % Favored : 95.68 % Rotamer: Outliers : 4.68 % Allowed : 17.28 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3840 helix: 0.36 (0.14), residues: 1440 sheet: -1.21 (0.27), residues: 312 loop : 0.02 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.009 0.001 TYR C 459 PHE 0.012 0.002 PHE G 35 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00447 (31080) covalent geometry : angle 0.61807 (42288) hydrogen bonds : bond 0.03588 ( 1168) hydrogen bonds : angle 4.86355 ( 3222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 326 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: A 337 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7915 (ptp) REVERT: B 112 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: B 337 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7916 (ptp) REVERT: C 112 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: C 337 MET cc_start: 0.7881 (mpp) cc_final: 0.7547 (ptp) REVERT: D 112 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: G 337 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7916 (ptp) REVERT: H 337 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7923 (ptp) outliers start: 148 outliers final: 90 residues processed: 421 average time/residue: 0.1656 time to fit residues: 116.7748 Evaluate side-chains 381 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 283 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 262 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 367 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN C 112 GLN C 334 GLN D 112 GLN D 303 ASN D 334 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133345 restraints weight = 33995.978| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.18 r_work: 0.3458 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 31080 Z= 0.132 Angle : 0.570 6.499 42288 Z= 0.285 Chirality : 0.044 0.142 4896 Planarity : 0.004 0.035 5208 Dihedral : 15.420 144.138 5136 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 5.06 % Allowed : 17.06 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.14), residues: 3840 helix: 0.48 (0.14), residues: 1440 sheet: -1.08 (0.28), residues: 312 loop : 0.10 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 412 TYR 0.008 0.001 TYR C 348 PHE 0.009 0.001 PHE G 35 HIS 0.002 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00322 (31080) covalent geometry : angle 0.56981 (42288) hydrogen bonds : bond 0.03089 ( 1168) hydrogen bonds : angle 4.69729 ( 3222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 357 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: A 272 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8761 (p) REVERT: A 384 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8708 (m) REVERT: B 384 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 112 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: C 179 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8131 (ptt) REVERT: C 272 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8781 (p) REVERT: C 384 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8702 (m) REVERT: D 112 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: D 325 MET cc_start: 0.9215 (ttt) cc_final: 0.8979 (ttt) REVERT: D 384 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8713 (m) REVERT: E 272 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8750 (p) REVERT: E 325 MET cc_start: 0.9217 (ttt) cc_final: 0.9003 (ttt) REVERT: F 272 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (p) REVERT: G 272 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (p) REVERT: H 272 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8740 (p) outliers start: 160 outliers final: 97 residues processed: 468 average time/residue: 0.1867 time to fit residues: 142.6601 Evaluate side-chains 414 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 303 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 281 optimal weight: 9.9990 chunk 17 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135169 restraints weight = 33654.496| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.17 r_work: 0.3173 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31080 Z= 0.113 Angle : 0.556 7.092 42288 Z= 0.278 Chirality : 0.043 0.139 4896 Planarity : 0.004 0.036 5208 Dihedral : 15.092 143.148 5136 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.80 % Favored : 95.99 % Rotamer: Outliers : 4.43 % Allowed : 18.89 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3840 helix: 0.64 (0.14), residues: 1448 sheet: -0.47 (0.31), residues: 272 loop : 0.06 (0.15), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 136 TYR 0.007 0.001 TYR H 348 PHE 0.008 0.001 PHE H 35 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00273 (31080) covalent geometry : angle 0.55565 (42288) hydrogen bonds : bond 0.02858 ( 1168) hydrogen bonds : angle 4.56891 ( 3222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 323 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7994 (ptt) REVERT: A 272 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8674 (p) REVERT: B 179 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7976 (ptt) REVERT: B 272 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8669 (p) REVERT: C 272 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 179 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7985 (ptt) REVERT: E 206 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7331 (mmtp) REVERT: E 272 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8664 (p) REVERT: E 384 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8616 (m) REVERT: F 94 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8701 (t0) REVERT: F 206 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7347 (mmtp) REVERT: F 272 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (p) REVERT: F 384 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8598 (m) REVERT: G 272 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8669 (p) REVERT: H 206 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7351 (mmtp) REVERT: H 272 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8669 (p) outliers start: 140 outliers final: 103 residues processed: 412 average time/residue: 0.1641 time to fit residues: 111.9566 Evaluate side-chains 414 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 295 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 204 optimal weight: 0.4980 chunk 363 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN C 112 GLN C 334 GLN C 441 GLN D 112 GLN D 303 ASN D 334 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134007 restraints weight = 33716.936| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.17 r_work: 0.3427 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31080 Z= 0.125 Angle : 0.559 7.376 42288 Z= 0.279 Chirality : 0.043 0.139 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.013 142.083 5136 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.49 % Favored : 96.30 % Rotamer: Outliers : 5.13 % Allowed : 18.80 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3840 helix: 0.70 (0.14), residues: 1448 sheet: -0.43 (0.31), residues: 272 loop : 0.04 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 136 TYR 0.008 0.001 TYR A 348 PHE 0.009 0.001 PHE E 35 HIS 0.009 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00307 (31080) covalent geometry : angle 0.55946 (42288) hydrogen bonds : bond 0.02947 ( 1168) hydrogen bonds : angle 4.53316 ( 3222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 302 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: A 179 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8012 (ptt) REVERT: A 384 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 179 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8004 (ptt) REVERT: B 272 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 384 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8727 (m) REVERT: C 112 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: C 179 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8051 (ptt) REVERT: C 272 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8771 (p) REVERT: C 384 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8725 (m) REVERT: D 112 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: D 179 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7992 (ptt) REVERT: E 136 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7407 (ttm-80) REVERT: E 206 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7444 (mmtp) REVERT: E 272 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (p) REVERT: F 136 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7386 (ttm-80) REVERT: F 206 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7451 (mmtp) REVERT: F 272 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8767 (p) REVERT: F 384 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8673 (m) REVERT: G 136 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7401 (ttm-80) REVERT: G 272 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8766 (p) REVERT: H 136 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7412 (ttm-80) REVERT: H 206 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7460 (mmtp) REVERT: H 272 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8763 (p) outliers start: 162 outliers final: 125 residues processed: 413 average time/residue: 0.1693 time to fit residues: 116.2394 Evaluate side-chains 432 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 287 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 321 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 286 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 235 optimal weight: 0.6980 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 112 GLN C 303 ASN D 112 GLN D 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135241 restraints weight = 33778.223| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.17 r_work: 0.3397 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31080 Z= 0.107 Angle : 0.546 7.862 42288 Z= 0.271 Chirality : 0.042 0.137 4896 Planarity : 0.004 0.034 5208 Dihedral : 14.806 141.656 5136 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 5.09 % Allowed : 18.89 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3840 helix: 0.84 (0.14), residues: 1448 sheet: -0.28 (0.32), residues: 272 loop : 0.09 (0.15), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 136 TYR 0.007 0.001 TYR H 348 PHE 0.007 0.001 PHE E 35 HIS 0.002 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00259 (31080) covalent geometry : angle 0.54553 (42288) hydrogen bonds : bond 0.02754 ( 1168) hydrogen bonds : angle 4.46836 ( 3222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 305 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: A 179 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7946 (ptt) REVERT: A 272 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 179 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7931 (ptt) REVERT: B 272 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 112 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: C 179 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8006 (ptt) REVERT: D 112 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: D 179 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7928 (ptt) REVERT: E 179 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8020 (ptt) REVERT: E 272 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8720 (p) REVERT: F 272 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8722 (p) REVERT: F 384 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8614 (m) REVERT: G 179 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8007 (ptt) REVERT: G 272 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8719 (p) REVERT: H 179 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8022 (ptt) REVERT: H 272 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8717 (p) outliers start: 161 outliers final: 127 residues processed: 411 average time/residue: 0.1682 time to fit residues: 114.3010 Evaluate side-chains 432 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 288 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 371 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 144 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 283 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 112 GLN C 303 ASN D 94 ASN D 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 303 ASN G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135005 restraints weight = 33683.855| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.18 r_work: 0.3228 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31080 Z= 0.109 Angle : 0.545 7.590 42288 Z= 0.271 Chirality : 0.043 0.137 4896 Planarity : 0.003 0.034 5208 Dihedral : 14.707 141.220 5136 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 5.13 % Allowed : 18.54 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3840 helix: 0.89 (0.14), residues: 1448 sheet: -0.23 (0.32), residues: 272 loop : 0.10 (0.15), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 136 TYR 0.007 0.001 TYR H 348 PHE 0.008 0.001 PHE E 35 HIS 0.002 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00264 (31080) covalent geometry : angle 0.54506 (42288) hydrogen bonds : bond 0.02748 ( 1168) hydrogen bonds : angle 4.45617 ( 3222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 294 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: A 179 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7872 (ptt) REVERT: A 272 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8682 (p) REVERT: B 179 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7820 (ptt) REVERT: B 272 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8677 (p) REVERT: C 112 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: C 179 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7895 (ptt) REVERT: D 94 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8819 (t0) REVERT: D 112 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: D 179 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7844 (ptt) REVERT: E 179 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7859 (ptt) REVERT: E 272 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8679 (p) REVERT: F 179 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: F 272 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8682 (p) REVERT: G 179 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7857 (ptt) REVERT: G 272 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8685 (p) REVERT: H 179 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7867 (ptt) REVERT: H 272 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8691 (p) outliers start: 162 outliers final: 129 residues processed: 399 average time/residue: 0.1857 time to fit residues: 123.1557 Evaluate side-chains 435 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 288 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 290 optimal weight: 0.9980 chunk 338 optimal weight: 0.1980 chunk 152 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 195 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 112 GLN C 303 ASN D 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 303 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135602 restraints weight = 33435.671| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.18 r_work: 0.3429 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31080 Z= 0.104 Angle : 0.543 7.572 42288 Z= 0.270 Chirality : 0.042 0.136 4896 Planarity : 0.004 0.036 5208 Dihedral : 14.585 140.857 5136 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 4.75 % Allowed : 19.08 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.14), residues: 3840 helix: 0.94 (0.14), residues: 1448 sheet: -0.18 (0.32), residues: 272 loop : 0.11 (0.15), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 136 TYR 0.013 0.001 TYR G 411 PHE 0.007 0.001 PHE E 35 HIS 0.002 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00252 (31080) covalent geometry : angle 0.54300 (42288) hydrogen bonds : bond 0.02697 ( 1168) hydrogen bonds : angle 4.42992 ( 3222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 299 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: A 179 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7893 (ptt) REVERT: A 272 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 179 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7912 (ptt) REVERT: B 272 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8710 (p) REVERT: C 112 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: C 136 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7377 (ttm-80) REVERT: C 179 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7902 (ptt) REVERT: D 112 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: D 179 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7832 (ptt) REVERT: E 136 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7348 (ttm-80) REVERT: E 179 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7899 (ptt) REVERT: E 272 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (p) REVERT: F 136 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7328 (ttm-80) REVERT: F 179 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7883 (ptt) REVERT: F 272 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8702 (p) REVERT: G 136 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7331 (ttm-80) REVERT: G 179 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7937 (ptt) REVERT: G 272 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8709 (p) REVERT: H 136 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7328 (ttm-80) REVERT: H 179 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7938 (ptt) REVERT: H 272 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8719 (p) outliers start: 150 outliers final: 127 residues processed: 393 average time/residue: 0.1893 time to fit residues: 123.3328 Evaluate side-chains 431 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 287 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 329 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 321 optimal weight: 0.3980 chunk 201 optimal weight: 0.9990 chunk 328 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 112 GLN C 303 ASN D 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135634 restraints weight = 33729.307| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.17 r_work: 0.3407 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31080 Z= 0.105 Angle : 0.548 8.321 42288 Z= 0.271 Chirality : 0.042 0.136 4896 Planarity : 0.004 0.035 5208 Dihedral : 14.461 140.284 5136 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 4.68 % Allowed : 19.24 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.14), residues: 3840 helix: 0.97 (0.14), residues: 1448 sheet: -0.16 (0.33), residues: 272 loop : 0.09 (0.15), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 136 TYR 0.012 0.001 TYR H 411 PHE 0.007 0.001 PHE E 35 HIS 0.002 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00255 (31080) covalent geometry : angle 0.54760 (42288) hydrogen bonds : bond 0.02674 ( 1168) hydrogen bonds : angle 4.42156 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6482.23 seconds wall clock time: 112 minutes 18.79 seconds (6738.79 seconds total)