Starting phenix.real_space_refine on Sat Aug 8 22:18:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7q_41989/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.cif" model { file = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_2026/8u7q_41989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7q_41989/08_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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "E" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "F" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "G" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 6.22, per 1000 atoms: 0.20 Number of scatterers: 30520 At special positions: 0 Unit cell: (151.96, 151.96, 112.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 6056 8.00 N 5192 7.00 C 18992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.136A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.322A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.319A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.166A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 84 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.139A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.297A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 84 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.138A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 84 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 256 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.341A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.678A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER A 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.626A pdb=" N SER D 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER B 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.566A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.632A pdb=" N SER C 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU E 209 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE E 221 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER E 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 509 through 510 removed outlier: 3.616A pdb=" N SER H 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER F 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER G 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9523 1.34 - 1.45: 3862 1.45 - 1.57: 17231 1.57 - 1.69: 152 1.69 - 1.81: 312 Bond restraints: 31080 Sorted by residual: bond pdb=" N VAL C 350 " pdb=" CA VAL C 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.85e+01 bond pdb=" N VAL B 350 " pdb=" CA VAL B 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.83e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.53e+01 bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 31075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 41256 3.13 - 6.26: 807 6.26 - 9.39: 139 9.39 - 12.52: 70 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: 17832 33.95 - 67.89: 919 67.89 - 101.84: 169 101.84 - 135.79: 6 135.79 - 169.73: 26 Dihedral angle restraints: 18952 sinusoidal: 8008 harmonic: 10944 Sorted by residual: dihedral pdb=" O3B GTP F 601 " pdb=" O3A GTP F 601 " pdb=" PB GTP F 601 " pdb=" PA GTP F 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.81 -169.73 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PB GTP G 601 " pdb=" PA GTP G 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.59 -169.51 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.17 163.76 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 18949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4300 0.077 - 0.154: 476 0.154 - 0.231: 37 0.231 - 0.308: 21 0.308 - 0.385: 62 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: 0.07 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.730 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.140 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31080 Z= 0.286 Angle : 1.116 15.647 42288 Z= 0.583 Chirality : 0.064 0.385 4896 Planarity : 0.005 0.073 5208 Dihedral : 20.762 169.733 11976 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 0.73 % Allowed : 15.98 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 0.00570 / 0.29 (31080) covalent geometry : angle 1.11556 / 0.58 (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 : 1.106 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: 0.1925 time to fit residues: 124.6511 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 : 0.965 ------------------------------------------------------------------------------- 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... 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 = 0.3878 r_free = 0.3878 target = 0.158199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138687 restraints weight = 34230.385| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.15 r_work: 0.3155 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31080 Z= 0.141 Angle : 0.661 7.554 42288 Z= 0.324 Chirality : 0.047 0.261 4896 Planarity : 0.004 0.050 5208 Dihedral : 17.729 149.505 5138 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 2.15 % Allowed : 17.44 % Favored : 80.41 % 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: -0.20 (0.14), residues: 3840 helix: 0.33 (0.14), residues: 1416 sheet: -1.77 (0.24), residues: 424 loop : 0.06 (0.15), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 341 TYR 0.007 0.001 TYR D 459 PHE 0.008 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 0.66079 / 0.32 (42288) hydrogen bonds : bond 0.03348 / 2.26 ( 1168) hydrogen bonds : angle 5.16358 / 3.62 ( 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 476 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 408 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 MET cc_start: 0.7721 (mpp) cc_final: 0.7464 (ptp) outliers start: 68 outliers final: 45 residues processed: 438 average time/residue: 0.1759 time to fit residues: 128.5914 Evaluate side-chains 367 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 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 183 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 31 optimal weight: 0.7980 chunk 335 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 112 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 300 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 237 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 303 ASN A 368 GLN B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 230 ASN B 303 ASN B 368 GLN C 94 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 230 ASN C 303 ASN C 368 GLN D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 303 ASN D 368 GLN E 112 GLN E 230 ASN E 303 ASN E 368 GLN F 230 ASN F 303 ASN F 368 GLN G 230 ASN G 303 ASN G 368 GLN H 112 GLN H 230 ASN H 303 ASN H 368 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140665 restraints weight = 34054.969| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.12 r_work: 0.3518 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31080 Z= 0.109 Angle : 0.580 6.656 42288 Z= 0.287 Chirality : 0.044 0.190 4896 Planarity : 0.004 0.039 5208 Dihedral : 16.198 147.803 5136 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 3.89 % Allowed : 17.85 % Favored : 78.26 % 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: 0.16 (0.14), residues: 3840 helix: 0.57 (0.14), residues: 1432 sheet: -1.72 (0.26), residues: 344 loop : 0.26 (0.15), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 412 TYR 0.007 0.001 TYR B 411 PHE 0.006 0.001 PHE E 35 HIS 0.006 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (31080) covalent geometry : angle 0.57991 / 0.29 (42288) hydrogen bonds : bond 0.02985 / 2.01 ( 1168) hydrogen bonds : angle 4.79155 / 3.36 ( 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 473 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 350 time to evaluate : 1.016 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 337 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7294 (ptp) REVERT: B 337 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7324 (ptp) REVERT: C 337 MET cc_start: 0.7829 (mpp) cc_final: 0.7362 (ptp) REVERT: D 337 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7327 (ptp) REVERT: G 337 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7321 (ptp) outliers start: 123 outliers final: 70 residues processed: 414 average time/residue: 0.1748 time to fit residues: 122.7642 Evaluate side-chains 393 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain 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 116 THR 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 116 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL 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 C residue 448 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL 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 D residue 448 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 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 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 G residue 448 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR 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: 0.9980 chunk 369 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 303 ASN A 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 507 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 507 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 303 ASN D 507 HIS E 171 HIS E 303 ASN E 507 HIS F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 303 ASN F 507 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 303 ASN G 507 HIS H 171 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131592 restraints weight = 34146.455| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.17 r_work: 0.3434 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31080 Z= 0.169 Angle : 0.622 8.043 42288 Z= 0.310 Chirality : 0.046 0.157 4896 Planarity : 0.004 0.035 5208 Dihedral : 15.674 145.400 5136 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Rotamer: Outliers : 4.27 % Allowed : 17.53 % Favored : 78.20 % 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: 0.04 (0.14), residues: 3840 helix: 0.39 (0.14), residues: 1448 sheet: -1.15 (0.27), residues: 312 loop : 0.10 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 322 TYR 0.011 0.001 TYR B 348 PHE 0.015 0.002 PHE H 110 HIS 0.005 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (31080) covalent geometry : angle 0.62163 / 0.31 (42288) hydrogen bonds : bond 0.03565 / 2.38 ( 1168) hydrogen bonds : angle 4.83067 / 3.38 ( 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 478 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 343 time to evaluate : 1.181 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 337 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7884 (ptp) REVERT: C 337 MET cc_start: 0.7834 (mpp) cc_final: 0.7510 (ptp) REVERT: D 337 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7854 (ptp) REVERT: G 337 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (ptp) outliers start: 135 outliers final: 93 residues processed: 424 average time/residue: 0.1834 time to fit residues: 130.6845 Evaluate side-chains 376 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 155 VAL 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 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 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 386 MET 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 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 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 155 VAL 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 330 ILE Chi-restraints excluded: chain D residue 337 MET 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 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 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 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 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 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 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 317 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 303 ASN ** 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 E 334 GLN F 94 ASN ** F 112 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 303 ASN G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130044 restraints weight = 34130.994| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.17 r_work: 0.3415 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31080 Z= 0.177 Angle : 0.630 8.506 42288 Z= 0.311 Chirality : 0.047 0.176 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.389 144.148 5136 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Rotamer: Outliers : 4.91 % Allowed : 17.56 % Favored : 77.53 % 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: -0.09 (0.14), residues: 3840 helix: 0.33 (0.14), residues: 1448 sheet: -1.19 (0.27), residues: 312 loop : -0.03 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 412 TYR 0.008 0.001 TYR A 459 PHE 0.012 0.002 PHE H 35 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (31080) covalent geometry : angle 0.63037 / 0.31 (42288) hydrogen bonds : bond 0.03449 / 2.31 ( 1168) hydrogen bonds : angle 4.79856 / 3.36 ( 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 486 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 331 time to evaluate : 1.157 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 136 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7162 (ttm-80) REVERT: C 179 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8240 (ptt) REVERT: C 337 MET cc_start: 0.7771 (mpp) cc_final: 0.7459 (ptp) REVERT: E 94 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8795 (t0) REVERT: F 94 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (t0) REVERT: F 136 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7199 (ttm-80) REVERT: G 94 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8821 (t0) outliers start: 155 outliers final: 105 residues processed: 440 average time/residue: 0.1961 time to fit residues: 142.0108 Evaluate side-chains 380 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 271 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 305 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 B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 305 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 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 305 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 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 155 VAL Chi-restraints excluded: chain D residue 158 VAL 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 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 94 ASN 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 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 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 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 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 305 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 444 SER 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 305 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 444 SER 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: 7.9990 chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 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** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131183 restraints weight = 33905.678| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.19 r_work: 0.3422 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31080 Z= 0.149 Angle : 0.600 6.989 42288 Z= 0.297 Chirality : 0.045 0.146 4896 Planarity : 0.004 0.038 5208 Dihedral : 15.213 143.695 5136 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 4.40 % Allowed : 19.27 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3840 helix: 0.44 (0.14), residues: 1440 sheet: -1.10 (0.27), residues: 312 loop : -0.04 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 136 TYR 0.008 0.001 TYR B 348 PHE 0.009 0.001 PHE E 35 HIS 0.002 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (31080) covalent geometry : angle 0.60022 / 0.30 (42288) hydrogen bonds : bond 0.03211 / 2.15 ( 1168) hydrogen bonds : angle 4.69596 / 3.28 ( 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 433 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 294 time to evaluate : 0.969 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: 0.8588 (OUTLIER) cc_final: 0.8132 (ptt) REVERT: A 272 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8817 (p) REVERT: B 179 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8137 (ptt) REVERT: B 272 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8825 (p) REVERT: C 136 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.7145 (ttm-80) REVERT: C 337 MET cc_start: 0.7721 (mpp) cc_final: 0.7451 (ptp) REVERT: D 179 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8113 (ptt) REVERT: E 206 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7544 (mmtp) REVERT: E 272 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8802 (p) REVERT: F 206 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7550 (mmtp) REVERT: F 272 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (p) REVERT: G 206 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7551 (mmtp) REVERT: G 272 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8799 (p) REVERT: H 94 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (t0) REVERT: H 206 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7546 (mmtp) REVERT: H 272 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8796 (p) outliers start: 139 outliers final: 95 residues processed: 383 average time/residue: 0.1856 time to fit residues: 116.6325 Evaluate side-chains 383 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 274 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 272 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 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 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 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL 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 C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE 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 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 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 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 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET 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 206 LYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 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 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 206 LYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 204 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 303 ASN ** D 112 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 E 334 GLN ** 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 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131186 restraints weight = 33903.210| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.18 r_work: 0.3425 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3101 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= 0.137 Angle : 0.592 7.359 42288 Z= 0.291 Chirality : 0.044 0.143 4896 Planarity : 0.004 0.037 5208 Dihedral : 15.008 142.961 5136 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.02 % Rotamer: Outliers : 4.84 % Allowed : 18.99 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3840 helix: 0.53 (0.14), residues: 1448 sheet: -0.97 (0.28), residues: 312 loop : -0.05 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 136 TYR 0.008 0.001 TYR D 348 PHE 0.010 0.001 PHE H 99 HIS 0.009 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (31080) covalent geometry : angle 0.59226 / 0.29 (42288) hydrogen bonds : bond 0.03076 / 2.06 ( 1168) hydrogen bonds : angle 4.62722 / 3.24 ( 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 430 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 277 time to evaluate : 1.130 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: 0.8566 (OUTLIER) cc_final: 0.8061 (ptt) REVERT: A 272 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 179 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8093 (ptt) REVERT: B 272 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 136 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7189 (ttm-80) REVERT: C 179 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8095 (ptt) REVERT: D 179 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8063 (ptt) REVERT: E 179 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8103 (ptt) REVERT: E 272 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8790 (p) REVERT: F 136 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7465 (ttm-80) REVERT: F 272 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8792 (p) REVERT: G 179 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8100 (ptt) REVERT: G 272 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8784 (p) REVERT: H 179 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8079 (ptt) REVERT: H 272 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8794 (p) outliers start: 153 outliers final: 115 residues processed: 376 average time/residue: 0.1946 time to fit residues: 120.3861 Evaluate side-chains 406 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 278 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 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 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 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 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 E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 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 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 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL 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 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 303 ASN Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL 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: 0.9990 chunk 251 optimal weight: 3.9990 chunk 196 optimal weight: 0.0170 chunk 286 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 303 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 441 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 303 ASN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 303 ASN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS H 303 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133128 restraints weight = 33868.882| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.17 r_work: 0.3375 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31080 Z= 0.109 Angle : 0.570 7.745 42288 Z= 0.279 Chirality : 0.043 0.140 4896 Planarity : 0.004 0.037 5208 Dihedral : 14.773 142.670 5136 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.44 % Favored : 96.35 % Rotamer: Outliers : 4.97 % Allowed : 18.64 % Favored : 76.39 % 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: 0.22 (0.14), residues: 3840 helix: 0.70 (0.14), residues: 1448 sheet: -0.81 (0.29), residues: 312 loop : 0.03 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 136 TYR 0.007 0.001 TYR B 348 PHE 0.007 0.001 PHE H 35 HIS 0.002 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (31080) covalent geometry : angle 0.56991 / 0.28 (42288) hydrogen bonds : bond 0.02831 / 1.89 ( 1168) hydrogen bonds : angle 4.54302 / 3.18 ( 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 447 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 290 time to evaluate : 1.147 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: 0.8562 (OUTLIER) cc_final: 0.8004 (ptt) REVERT: A 272 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8762 (p) REVERT: B 179 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8005 (ptt) REVERT: B 272 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8756 (p) REVERT: C 179 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8010 (ptt) REVERT: D 179 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7999 (ptt) REVERT: E 94 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8873 (t0) REVERT: E 179 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8064 (ptt) REVERT: E 272 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8755 (p) REVERT: F 179 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8052 (ptt) REVERT: F 272 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8740 (p) REVERT: G 94 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8872 (t0) REVERT: G 272 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8754 (p) REVERT: H 179 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8045 (ptt) REVERT: H 272 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8747 (p) outliers start: 157 outliers final: 115 residues processed: 396 average time/residue: 0.1865 time to fit residues: 122.4316 Evaluate side-chains 405 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 275 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 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 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 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 303 ASN 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 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 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 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN 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 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 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 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 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 303 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 371 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 303 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS 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 ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 303 ASN G 334 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132769 restraints weight = 33845.028| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.19 r_work: 0.3393 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31080 Z= 0.121 Angle : 0.580 7.475 42288 Z= 0.283 Chirality : 0.043 0.139 4896 Planarity : 0.004 0.037 5208 Dihedral : 14.693 142.044 5136 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 4.43 % Allowed : 18.99 % Favored : 76.58 % 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: 0.26 (0.14), residues: 3840 helix: 0.75 (0.14), residues: 1448 sheet: -0.78 (0.29), residues: 312 loop : 0.02 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 136 TYR 0.007 0.001 TYR B 348 PHE 0.008 0.001 PHE H 35 HIS 0.003 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (31080) covalent geometry : angle 0.57958 / 0.28 (42288) hydrogen bonds : bond 0.02880 / 1.92 ( 1168) hydrogen bonds : angle 4.52021 / 3.16 ( 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 435 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 295 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: 0.8552 (OUTLIER) cc_final: 0.7925 (ptt) REVERT: A 272 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (p) REVERT: B 179 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7934 (ptt) REVERT: C 136 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7330 (ttm-80) REVERT: C 179 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7954 (ptt) REVERT: D 179 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7910 (ptt) REVERT: E 179 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8036 (ptt) REVERT: E 272 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8758 (p) REVERT: F 179 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8004 (ptt) REVERT: F 272 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (p) REVERT: G 179 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8008 (ptt) REVERT: G 272 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8754 (p) REVERT: H 179 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8014 (ptt) REVERT: H 272 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8754 (p) outliers start: 140 outliers final: 114 residues processed: 383 average time/residue: 0.1891 time to fit residues: 119.6775 Evaluate side-chains 410 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 283 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 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 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 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 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 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 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET 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 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN 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 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 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 303 ASN 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: 0.9990 chunk 338 optimal weight: 0.0670 chunk 152 optimal weight: 0.0570 chunk 229 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 334 GLN B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 94 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 334 GLN ** 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 H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134967 restraints weight = 33429.112| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.17 r_work: 0.3476 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31080 Z= 0.100 Angle : 0.569 7.562 42288 Z= 0.277 Chirality : 0.043 0.135 4896 Planarity : 0.004 0.037 5208 Dihedral : 14.429 141.740 5136 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.07 % Favored : 96.72 % Rotamer: Outliers : 4.02 % Allowed : 19.49 % Favored : 76.49 % 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: 0.40 (0.14), residues: 3840 helix: 0.94 (0.14), residues: 1448 sheet: -0.70 (0.29), residues: 312 loop : 0.05 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 136 TYR 0.013 0.001 TYR H 411 PHE 0.006 0.001 PHE E 35 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (31080) covalent geometry : angle 0.56921 / 0.28 (42288) hydrogen bonds : bond 0.02666 / 1.78 ( 1168) hydrogen bonds : angle 4.44888 / 3.12 ( 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 430 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 303 time to evaluate : 1.182 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 94 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8859 (t0) REVERT: A 179 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7842 (ptt) REVERT: A 272 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 94 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8854 (t0) REVERT: B 179 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7841 (ptt) REVERT: B 272 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 136 ARG cc_start: 0.7621 (ttm110) cc_final: 0.7357 (ttm-80) REVERT: C 179 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7884 (ptt) REVERT: D 179 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7835 (ptt) REVERT: E 272 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8724 (p) REVERT: F 179 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7891 (ptt) REVERT: F 272 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8719 (p) REVERT: G 179 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7933 (ptt) REVERT: G 272 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8720 (p) REVERT: H 272 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8733 (p) outliers start: 127 outliers final: 111 residues processed: 381 average time/residue: 0.1875 time to fit residues: 117.9952 Evaluate side-chains 395 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 270 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 94 ASN 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 272 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 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 C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 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 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 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR 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 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 179 MET 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 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET 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 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 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 94 ASN Chi-restraints excluded: chain H residue 96 THR 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: 0.0670 chunk 146 optimal weight: 0.8980 chunk 312 optimal weight: 0.0070 chunk 329 optimal weight: 8.9990 chunk 160 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 179 optimal weight: 0.4980 chunk 199 optimal weight: 1.9990 chunk 321 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 328 optimal weight: 7.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 334 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 334 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136696 restraints weight = 33585.930| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.16 r_work: 0.3495 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31080 Z= 0.094 Angle : 0.561 7.634 42288 Z= 0.272 Chirality : 0.042 0.133 4896 Planarity : 0.004 0.038 5208 Dihedral : 14.230 140.893 5136 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.10 % Favored : 96.69 % Rotamer: Outliers : 3.70 % Allowed : 19.91 % Favored : 76.39 % 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: 0.60 (0.14), residues: 3840 helix: 1.09 (0.15), residues: 1448 sheet: -0.08 (0.35), residues: 232 loop : 0.07 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 136 TYR 0.012 0.001 TYR H 411 PHE 0.005 0.001 PHE G 35 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (31080) covalent geometry : angle 0.56105 / 0.27 (42288) hydrogen bonds : bond 0.02512 / 1.68 ( 1168) hydrogen bonds : angle 4.41126 / 3.09 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6805.75 seconds wall clock time: 117 minutes 46.52 seconds (7066.52 seconds total)