Starting phenix.real_space_refine on Sat Jun 6 18:31:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_41989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_41989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_41989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_41989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2026/8u7q_41989.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 7.74, per 1000 atoms: 0.25 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: 2.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.16 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: 7.11 Time building geometry restraints manager: 3.25 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=" O5' IMP G 603 " pdb=" P IMP G 603 " ideal model delta sigma weight residual 1.683 1.577 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" O5' IMP F 603 " pdb=" P IMP F 603 " ideal model delta sigma weight residual 1.683 1.577 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" O5' IMP C 603 " pdb=" P IMP C 603 " ideal model delta sigma weight residual 1.683 1.577 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O5' IMP D 603 " pdb=" P IMP D 603 " ideal model delta sigma weight residual 1.683 1.577 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " ideal model delta sigma weight residual 1.683 1.577 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 31075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 41384 3.13 - 6.26: 723 6.26 - 9.39: 111 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: 17864 33.95 - 67.89: 975 67.89 - 101.84: 209 101.84 - 135.79: 6 135.79 - 169.73: 26 Dihedral angle restraints: 19080 sinusoidal: 8136 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 19077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4300 0.077 - 0.154: 476 0.154 - 0.231: 45 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: 0.05 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: 5.870 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.970 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- 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 0.106 31080 Z= 0.285 Angle : 1.058 15.647 42288 Z= 0.571 Chirality : 0.063 0.385 4896 Planarity : 0.005 0.073 5208 Dihedral : 21.776 169.733 12104 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 are 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/Z covalent geometry : bond 0.00569 / 0.29 (31080) covalent geometry : angle 1.05823 / 0.57 (42288) hydrogen bonds : bond 0.15891 / 10.92 ( 1168) hydrogen bonds : angle 6.94131 / 4.90 ( 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 : 0.982 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: 0.1836 time to fit residues: 117.9838 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 : 1.035 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138813 restraints weight = 34236.358| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.13 r_work: 0.3507 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1228 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= 0.140 Angle : 0.640 6.108 42288 Z= 0.318 Chirality : 0.046 0.169 4896 Planarity : 0.004 0.051 5208 Dihedral : 18.999 150.562 5266 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.88 % Favored : 95.91 % Rotamer: Outliers : 1.96 % Allowed : 17.72 % Favored : 80.32 % 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 are not related in a simple way. whole: -0.23 (0.14), residues: 3840 helix: 0.31 (0.14), residues: 1416 sheet: -1.72 (0.24), residues: 440 loop : 0.05 (0.15), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 341 TYR 0.007 0.001 TYR E 459 PHE 0.009 0.001 PHE G 35 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (31080) covalent geometry : angle 0.64008 / 0.32 (42288) hydrogen bonds : bond 0.03700 / 2.51 ( 1168) hydrogen bonds : angle 5.22239 / 3.66 ( 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 461 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 399 time to evaluate : 1.072 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: 0.7748 (mpp) cc_final: 0.7387 (ptp) outliers start: 62 outliers final: 41 residues processed: 428 average time/residue: 0.1711 time to fit residues: 121.6212 Evaluate side-chains 358 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 306 THR 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 306 THR 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 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 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 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 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: 0.0870 chunk 362 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 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: 0.6360 ------------------------------------------------------------------------------- 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 230 ASN A 368 GLN B 94 ASN B 112 GLN B 171 HIS B 230 ASN B 368 GLN C 94 ASN C 112 GLN C 171 HIS C 230 ASN C 368 GLN D 94 ASN D 112 GLN D 171 HIS D 230 ASN D 368 GLN E 171 HIS E 230 ASN E 368 GLN F 171 HIS F 230 ASN F 368 GLN G 171 HIS G 230 ASN G 368 GLN H 171 HIS H 230 ASN H 368 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139760 restraints weight = 34031.819| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.10 r_work: 0.3497 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1973 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= 0.116 Angle : 0.579 6.113 42288 Z= 0.289 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.040 5208 Dihedral : 16.023 148.304 5264 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 3.80 % Allowed : 18.04 % Favored : 78.16 % 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 are not related in a simple way. whole: 0.09 (0.14), residues: 3840 helix: 0.54 (0.14), residues: 1432 sheet: -1.72 (0.25), residues: 360 loop : 0.21 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 412 TYR 0.009 0.001 TYR D 411 PHE 0.007 0.001 PHE F 35 HIS 0.005 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (31080) covalent geometry : angle 0.57918 / 0.29 (42288) hydrogen bonds : bond 0.03042 / 2.05 ( 1168) hydrogen bonds : angle 4.74652 / 3.33 ( 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 462 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 342 time to evaluate : 1.215 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: 0.7516 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: A 337 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7400 (ptp) REVERT: B 112 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: B 337 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7406 (ptp) REVERT: C 112 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: C 337 MET cc_start: 0.7851 (mpp) cc_final: 0.7445 (ptp) REVERT: D 112 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: D 337 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7397 (ptp) REVERT: E 337 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7391 (ptp) REVERT: F 337 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7362 (ptp) REVERT: G 337 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7395 (ptp) REVERT: H 337 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7411 (ptp) outliers start: 120 outliers final: 59 residues processed: 415 average time/residue: 0.1642 time to fit residues: 115.6406 Evaluate side-chains 369 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 C residue 448 GLN 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 116 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL 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 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 337 MET 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 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 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL 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: 5.9990 chunk 369 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 244 optimal weight: 0.0670 chunk 318 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 171 HIS A 507 HIS B 112 GLN B 303 ASN B 507 HIS C 112 GLN C 303 ASN C 507 HIS D 112 GLN D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 507 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135223 restraints weight = 34055.498| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.18 r_work: 0.3483 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31080 Z= 0.132 Angle : 0.572 6.625 42288 Z= 0.285 Chirality : 0.044 0.143 4896 Planarity : 0.004 0.037 5208 Dihedral : 15.386 144.666 5264 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 4.43 % Allowed : 17.44 % Favored : 78.13 % 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 are not related in a simple way. whole: 0.14 (0.14), residues: 3840 helix: 0.57 (0.14), residues: 1440 sheet: -1.56 (0.26), residues: 360 loop : 0.22 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 412 TYR 0.008 0.001 TYR C 348 PHE 0.009 0.001 PHE H 35 HIS 0.005 0.001 HIS G 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (31080) covalent geometry : angle 0.57201 / 0.28 (42288) hydrogen bonds : bond 0.03102 / 2.08 ( 1168) hydrogen bonds : angle 4.69886 / 3.29 ( 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 473 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 333 time to evaluate : 1.211 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: B 325 MET cc_start: 0.9190 (ttt) cc_final: 0.8977 (ttt) REVERT: C 325 MET cc_start: 0.9165 (ttt) cc_final: 0.8934 (ttt) REVERT: C 337 MET cc_start: 0.7747 (mpp) cc_final: 0.7398 (ptp) REVERT: D 337 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7655 (ptp) REVERT: E 337 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7588 (ptp) REVERT: F 337 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (ptp) REVERT: G 325 MET cc_start: 0.9179 (ttt) cc_final: 0.8967 (ttt) REVERT: G 337 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (ptp) REVERT: H 325 MET cc_start: 0.9186 (ttt) cc_final: 0.8974 (ttt) REVERT: H 337 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7589 (ptp) outliers start: 140 outliers final: 86 residues processed: 413 average time/residue: 0.1655 time to fit residues: 116.0873 Evaluate side-chains 384 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 337 MET 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 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 337 MET 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 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 337 MET 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 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 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 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 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: 1.9990 chunk 294 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 303 ASN A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 334 GLN G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 94 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130751 restraints weight = 34245.939| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.17 r_work: 0.3421 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 31080 Z= 0.181 Angle : 0.611 6.664 42288 Z= 0.306 Chirality : 0.046 0.156 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.426 144.427 5264 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.39 % Rotamer: Outliers : 4.97 % Allowed : 16.99 % 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 are not related in a simple way. whole: -0.03 (0.14), residues: 3840 helix: 0.41 (0.14), residues: 1440 sheet: -1.14 (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 D 412 TYR 0.009 0.001 TYR B 459 PHE 0.012 0.002 PHE G 35 HIS 0.016 0.001 HIS B 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.18 (31080) covalent geometry : angle 0.61143 / 0.31 (42288) hydrogen bonds : bond 0.03533 / 2.36 ( 1168) hydrogen bonds : angle 4.76251 / 3.33 ( 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 508 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 351 time to evaluate : 1.158 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: 0.7903 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: A 412 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7882 (ptt180) REVERT: B 112 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: B 412 ARG cc_start: 0.8319 (ptp90) cc_final: 0.7900 (ptt180) REVERT: C 112 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: C 337 MET cc_start: 0.7839 (mpp) cc_final: 0.7334 (ptp) REVERT: C 412 ARG cc_start: 0.8314 (ptp90) cc_final: 0.7961 (ptt180) REVERT: D 112 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: E 272 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8792 (p) REVERT: F 272 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8798 (p) REVERT: G 272 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8796 (p) REVERT: H 272 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8799 (p) outliers start: 157 outliers final: 97 residues processed: 457 average time/residue: 0.1831 time to fit residues: 134.6937 Evaluate side-chains 403 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 298 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR 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 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 370 VAL Chi-restraints excluded: chain B residue 383 THR 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 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 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR 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 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 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 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR 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 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 370 VAL Chi-restraints excluded: chain F residue 383 THR 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 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 272 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 383 THR 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 272 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 383 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 281 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 303 ASN B 112 GLN C 112 GLN C 303 ASN D 112 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133659 restraints weight = 33796.020| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.17 r_work: 0.3423 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2777 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= 0.121 Angle : 0.564 6.871 42288 Z= 0.282 Chirality : 0.043 0.140 4896 Planarity : 0.004 0.037 5208 Dihedral : 14.977 143.674 5264 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.83 % Rotamer: Outliers : 4.81 % Allowed : 17.97 % Favored : 77.22 % 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 are not related in a simple way. whole: 0.17 (0.14), residues: 3840 helix: 0.59 (0.14), residues: 1448 sheet: -0.93 (0.28), residues: 312 loop : 0.07 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 136 TYR 0.016 0.001 TYR B 509 PHE 0.008 0.001 PHE G 35 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (31080) covalent geometry : angle 0.56389 / 0.28 (42288) hydrogen bonds : bond 0.02940 / 1.97 ( 1168) hydrogen bonds : angle 4.59791 / 3.21 ( 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 474 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 322 time to evaluate : 1.089 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: 0.7747 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: A 179 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8120 (ptt) REVERT: A 384 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8699 (m) REVERT: B 112 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 179 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8130 (ptt) REVERT: B 384 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8675 (m) REVERT: C 112 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: C 179 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (ptt) REVERT: C 384 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8668 (m) REVERT: D 112 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: D 179 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8104 (ptt) REVERT: D 384 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8689 (m) REVERT: E 272 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8737 (p) REVERT: F 272 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8739 (p) REVERT: G 94 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8751 (t0) REVERT: G 272 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8739 (p) REVERT: H 94 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8758 (t0) REVERT: H 272 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8756 (p) outliers start: 152 outliers final: 104 residues processed: 427 average time/residue: 0.1645 time to fit residues: 117.7070 Evaluate side-chains 415 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 293 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 303 ASN Chi-restraints excluded: chain A residue 330 ILE 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 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 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 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 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 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 370 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET 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 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 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 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 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 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 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 94 ASN 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 303 ASN 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 94 ASN 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 303 ASN 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: 0.7980 chunk 363 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 229 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 303 ASN B 112 GLN B 303 ASN C 112 GLN C 303 ASN C 441 GLN D 112 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 334 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134013 restraints weight = 33739.835| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.18 r_work: 0.3410 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2909 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= 0.115 Angle : 0.557 7.457 42288 Z= 0.278 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.036 5208 Dihedral : 14.784 142.802 5264 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 4.75 % Allowed : 18.58 % 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 are not related in a simple way. whole: 0.29 (0.14), residues: 3840 helix: 0.72 (0.14), residues: 1448 sheet: -0.73 (0.29), residues: 312 loop : 0.09 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 136 TYR 0.013 0.001 TYR B 509 PHE 0.008 0.001 PHE G 35 HIS 0.005 0.001 HIS C 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (31080) covalent geometry : angle 0.55722 / 0.28 (42288) hydrogen bonds : bond 0.02874 / 1.92 ( 1168) hydrogen bonds : angle 4.52226 / 3.17 ( 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 450 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 300 time to evaluate : 1.160 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: 0.7624 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 179 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8029 (ptt) REVERT: B 112 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: B 179 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8020 (ptt) REVERT: B 384 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8707 (m) REVERT: C 112 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: C 179 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8026 (ptt) REVERT: C 384 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8700 (m) REVERT: D 112 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: D 179 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8028 (ptt) REVERT: E 136 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7242 (ttm-80) REVERT: E 272 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8720 (p) REVERT: E 325 MET cc_start: 0.9325 (ttt) cc_final: 0.9123 (ttt) REVERT: F 136 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: F 272 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8737 (p) REVERT: G 136 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7226 (ttm-80) REVERT: G 272 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8722 (p) REVERT: H 136 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7231 (ttm-80) REVERT: H 272 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8725 (p) outliers start: 150 outliers final: 115 residues processed: 401 average time/residue: 0.1709 time to fit residues: 113.4476 Evaluate side-chains 418 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 289 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 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 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 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 321 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 C 112 GLN D 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 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** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133090 restraints weight = 33974.372| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.17 r_work: 0.3391 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3009 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= 0.130 Angle : 0.565 7.636 42288 Z= 0.282 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.036 5208 Dihedral : 14.745 141.909 5264 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 4.53 % Allowed : 18.64 % Favored : 76.84 % 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 are not related in a simple way. whole: 0.30 (0.14), residues: 3840 helix: 0.74 (0.14), residues: 1448 sheet: -0.68 (0.29), residues: 312 loop : 0.08 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 136 TYR 0.013 0.001 TYR B 509 PHE 0.010 0.001 PHE G 35 HIS 0.004 0.001 HIS C 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (31080) covalent geometry : angle 0.56450 / 0.28 (42288) hydrogen bonds : bond 0.02970 / 1.98 ( 1168) hydrogen bonds : angle 4.51758 / 3.16 ( 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 442 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 299 time to evaluate : 1.083 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: 0.7666 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: A 179 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8023 (ptt) REVERT: B 112 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: B 179 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8025 (ptt) REVERT: B 384 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8759 (m) REVERT: C 112 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: C 179 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8019 (ptt) REVERT: D 112 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: D 179 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8002 (ptt) REVERT: E 136 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7331 (ttm-80) REVERT: E 272 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8755 (p) REVERT: F 136 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7298 (ttm-80) REVERT: F 272 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8751 (p) REVERT: G 136 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7295 (ttm-80) REVERT: G 272 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (p) REVERT: H 136 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7309 (ttm-80) REVERT: H 272 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8759 (p) outliers start: 143 outliers final: 118 residues processed: 393 average time/residue: 0.1745 time to fit residues: 113.6419 Evaluate side-chains 418 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 287 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 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 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 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL 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: 0.6980 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 371 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 380 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 C 112 GLN C 303 ASN D 112 GLN D 334 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133160 restraints weight = 33828.039| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.19 r_work: 0.3413 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31080 Z= 0.123 Angle : 0.561 7.991 42288 Z= 0.279 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.036 5208 Dihedral : 14.635 141.947 5264 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 4.56 % Allowed : 18.42 % Favored : 77.03 % 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 are not related in a simple way. whole: 0.33 (0.14), residues: 3840 helix: 0.79 (0.14), residues: 1448 sheet: -0.68 (0.29), residues: 312 loop : 0.07 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 136 TYR 0.013 0.001 TYR B 509 PHE 0.008 0.001 PHE F 35 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.12 (31080) covalent geometry : angle 0.56073 / 0.28 (42288) hydrogen bonds : bond 0.02901 / 1.94 ( 1168) hydrogen bonds : angle 4.49852 / 3.15 ( 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 449 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 305 time to evaluate : 1.112 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: 0.7646 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: A 179 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7960 (ptt) REVERT: B 112 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: B 179 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8030 (ptt) REVERT: C 112 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: C 179 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7982 (ptt) REVERT: D 112 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: D 179 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7955 (ptt) REVERT: E 136 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7263 (ttm-80) REVERT: E 179 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8043 (ptt) REVERT: E 272 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8770 (p) REVERT: F 136 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7262 (ttm-80) REVERT: F 179 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8018 (ptt) REVERT: F 272 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8773 (p) REVERT: G 136 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7268 (ttm-80) REVERT: G 179 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8008 (ptt) REVERT: G 272 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8769 (p) REVERT: H 136 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7268 (ttm-80) REVERT: H 179 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8009 (ptt) REVERT: H 272 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8762 (p) outliers start: 144 outliers final: 111 residues processed: 397 average time/residue: 0.1726 time to fit residues: 112.9591 Evaluate side-chains 420 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 293 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 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 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 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 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 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 444 SER 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 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 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET 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 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 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET 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 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET 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: 1.9990 chunk 338 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 216 optimal weight: 0.0870 chunk 174 optimal weight: 0.6980 chunk 188 optimal weight: 0.0270 chunk 207 optimal weight: 0.0970 chunk 126 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- 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 C 94 ASN C 112 GLN C 303 ASN D 94 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** H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136423 restraints weight = 33408.515| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.17 r_work: 0.3455 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31080 Z= 0.094 Angle : 0.538 8.436 42288 Z= 0.266 Chirality : 0.042 0.134 4896 Planarity : 0.004 0.038 5208 Dihedral : 14.274 141.540 5264 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.12 % Favored : 96.67 % Rotamer: Outliers : 3.83 % Allowed : 19.34 % Favored : 76.84 % 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 are not related in a simple way. whole: 0.52 (0.14), residues: 3840 helix: 1.00 (0.15), residues: 1448 sheet: -0.56 (0.30), residues: 312 loop : 0.14 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 136 TYR 0.013 0.001 TYR C 509 PHE 0.005 0.001 PHE F 35 HIS 0.004 0.001 HIS C 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 (31080) covalent geometry : angle 0.53822 / 0.27 (42288) hydrogen bonds : bond 0.02576 / 1.72 ( 1168) hydrogen bonds : angle 4.40975 / 3.10 ( 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 445 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 324 time to evaluate : 1.145 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: 0.8508 (OUTLIER) cc_final: 0.7876 (ptt) REVERT: B 179 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7899 (ptt) REVERT: C 179 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7882 (ptt) REVERT: D 179 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7871 (ptt) REVERT: E 136 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: E 179 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7899 (ptt) REVERT: E 272 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8699 (p) REVERT: F 136 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7244 (ttm-80) REVERT: F 272 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8693 (p) REVERT: G 136 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: G 179 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7875 (ptt) REVERT: G 272 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8698 (p) REVERT: H 136 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7238 (ttm-80) REVERT: H 179 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7872 (ptt) REVERT: H 272 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8690 (p) outliers start: 121 outliers final: 101 residues processed: 395 average time/residue: 0.1703 time to fit residues: 112.1612 Evaluate side-chains 415 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 303 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 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 444 SER 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 179 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL 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 444 SER 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 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 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET 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 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 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 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 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 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR 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 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 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET 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 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 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET 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: 0.5980 chunk 146 optimal weight: 0.2980 chunk 312 optimal weight: 0.9980 chunk 329 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133795 restraints weight = 33738.694| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.20 r_work: 0.3455 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31080 Z= 0.118 Angle : 0.560 8.745 42288 Z= 0.278 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.035 5208 Dihedral : 14.205 139.870 5264 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.49 % Favored : 96.30 % Rotamer: Outliers : 3.99 % Allowed : 19.40 % Favored : 76.61 % 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 are not related in a simple way. whole: 0.44 (0.14), residues: 3840 helix: 0.99 (0.14), residues: 1440 sheet: -0.62 (0.30), residues: 312 loop : 0.06 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 136 TYR 0.013 0.001 TYR C 509 PHE 0.009 0.001 PHE B 490 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (31080) covalent geometry : angle 0.55960 / 0.28 (42288) hydrogen bonds : bond 0.02856 / 1.90 ( 1168) hydrogen bonds : angle 4.43746 / 3.11 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6639.33 seconds wall clock time: 114 minutes 55.48 seconds (6895.48 seconds total)