Starting phenix.real_space_refine on Fri Mar 6 10:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.map" model { file = "/net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7res_24438/03_2026/7res_24438.cif" } resolution = 3.05 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= 0.000 sd= 0.256 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 72 5.49 5 S 184 5.16 5 C 18768 2.51 5 N 5152 2.21 5 O 5912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "C" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "F" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "H" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.55, per 1000 atoms: 0.22 Number of scatterers: 30088 At special positions: 0 Unit cell: (135.45, 136.5, 142.8, 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 72 15.00 O 5912 8.00 N 5152 7.00 C 18768 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 32 sheets defined 40.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.512A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) 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 removed outlier: 3.630A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.953A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.525A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.617A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.608A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 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 502 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.518A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.886A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.645A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.616A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 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 502 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.503A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) 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 removed outlier: 3.636A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.918A pdb=" N LEU C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.638A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.608A pdb=" N VAL C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 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 502 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.515A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) 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 removed outlier: 3.623A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.911A pdb=" N LEU D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.656A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.610A pdb=" N VAL D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 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 502 Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.502A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) 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 removed outlier: 3.594A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.901A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.661A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.612A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 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 502 Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.507A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) 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 removed outlier: 3.620A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.797A pdb=" N LEU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.607A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 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 502 Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) 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 removed outlier: 3.703A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.816A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.647A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 333 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.614A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 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 502 Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.939A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.606A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 333 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.616A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 421 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 502 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 65 through 67 removed outlier: 3.526A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.733A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.661A pdb=" N SER A 403 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 403 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.794A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.813A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 403 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.816A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.829A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 403 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.524A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.818A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.528A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 208 through 211 removed outlier: 3.699A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.628A pdb=" N SER E 403 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.801A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 403 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.526A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 211 removed outlier: 3.829A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.812A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 403 " --> pdb=" O VAL G 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 208 through 211 removed outlier: 3.813A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 403 " --> pdb=" O VAL H 406 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 208 through 211 removed outlier: 3.698A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3078 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: 6.51 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4987 1.26 - 1.40: 6918 1.40 - 1.53: 17690 1.53 - 1.67: 669 1.67 - 1.81: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.84e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP H 601 " pdb=" C3' ATP H 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 40968 4.53 - 9.05: 367 9.05 - 13.58: 57 13.58 - 18.11: 59 18.11 - 22.64: 45 Bond angle restraints: 41496 Sorted by residual: angle pdb=" PB ATP G 601 " pdb=" O3B ATP G 601 " pdb=" PG ATP G 601 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.68 22.19 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 117.81 22.06 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 118.27 21.60 1.00e+00 1.00e+00 4.66e+02 ... (remaining 41491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 17871 32.92 - 65.84: 891 65.84 - 98.76: 133 98.76 - 131.68: 0 131.68 - 164.60: 1 Dihedral angle restraints: 18896 sinusoidal: 8040 harmonic: 10856 Sorted by residual: dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -3.47 -164.60 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual 123.40 140.08 -16.68 0 2.50e+00 1.60e-01 4.45e+01 dihedral pdb=" C THR A 10 " pdb=" N THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual -122.00 -136.36 14.36 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 18893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4730 0.136 - 0.273: 38 0.273 - 0.409: 30 0.409 - 0.545: 0 0.545 - 0.682: 2 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA THR A 10 " pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CB THR A 10 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TYR E 12 " pdb=" N TYR E 12 " pdb=" C TYR E 12 " pdb=" CB TYR E 12 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3B NAD H 604 " pdb=" C2B NAD H 604 " pdb=" C4B NAD H 604 " pdb=" O3B NAD H 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4797 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 12 " 0.033 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C TYR E 12 " -0.112 2.00e-02 2.50e+03 pdb=" O TYR E 12 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL E 13 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 12 " -0.010 2.00e-02 2.50e+03 3.27e-02 2.14e+01 pdb=" CG TYR E 12 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 12 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 12 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 12 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR E 12 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 12 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 12 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 8 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY A 8 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 8 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 9 " -0.011 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1601 2.70 - 3.25: 30769 3.25 - 3.80: 51427 3.80 - 4.35: 68032 4.35 - 4.90: 110806 Nonbonded interactions: 262635 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" O3' IMP C 603 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" O3' ATP F 602 " model vdw 2.188 3.040 nonbonded pdb=" O ALA D 396 " pdb=" NZ LYS D 409 " model vdw 2.188 3.120 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.188 2.432 nonbonded pdb=" O ALA A 396 " pdb=" NZ LYS A 409 " model vdw 2.189 3.120 ... (remaining 262630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.410 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.018 0.901 30593 Z= 1.173 Angle : 1.392 22.637 41496 Z= 0.939 Chirality : 0.060 0.682 4800 Planarity : 0.004 0.065 5160 Dihedral : 18.573 164.597 11984 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 4.87 % Allowed : 10.42 % Favored : 84.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.02 (0.12), residues: 3792 helix: -1.31 (0.12), residues: 1416 sheet: -1.25 (0.23), residues: 352 loop : -2.74 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 203 TYR 0.051 0.002 TYR E 12 PHE 0.010 0.002 PHE H 99 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.01697 (30592) covalent geometry : angle 1.39222 (41496) hydrogen bonds : bond 0.16453 ( 1090) hydrogen bonds : angle 7.36953 ( 3078) Misc. bond : bond 0.90091 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 603 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: A 91 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 146 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5503 (pp20) REVERT: A 224 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8225 (ttt-90) REVERT: A 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8754 (m-40) REVERT: A 355 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: A 441 GLN cc_start: 0.8501 (mt0) cc_final: 0.8233 (mt0) REVERT: A 449 ASP cc_start: 0.7538 (t70) cc_final: 0.6824 (t70) REVERT: B 161 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8208 (mtt180) REVERT: B 312 ASN cc_start: 0.9073 (m-40) cc_final: 0.8798 (m-40) REVERT: B 355 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8178 (ptt-90) REVERT: B 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7531 (mp0) REVERT: B 441 GLN cc_start: 0.8460 (mt0) cc_final: 0.8230 (mt0) REVERT: B 448 GLN cc_start: 0.7453 (tt0) cc_final: 0.7240 (tt0) REVERT: B 449 ASP cc_start: 0.7522 (t70) cc_final: 0.7116 (t70) REVERT: C 224 ARG cc_start: 0.8353 (ttt90) cc_final: 0.8138 (ttt-90) REVERT: C 312 ASN cc_start: 0.9050 (m-40) cc_final: 0.8745 (m-40) REVERT: C 355 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8030 (ptt-90) REVERT: D 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 146 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5379 (pp20) REVERT: D 161 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8485 (mtt180) REVERT: D 224 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8163 (ttt-90) REVERT: D 312 ASN cc_start: 0.9101 (m-40) cc_final: 0.8760 (m-40) REVERT: D 355 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: D 395 GLU cc_start: 0.7759 (mp0) cc_final: 0.7504 (mp0) REVERT: D 441 GLN cc_start: 0.8479 (mt0) cc_final: 0.8199 (mt0) REVERT: D 449 ASP cc_start: 0.7545 (t70) cc_final: 0.6855 (t70) REVERT: E 146 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: E 179 MET cc_start: 0.5193 (mtt) cc_final: 0.4979 (mtm) REVERT: E 224 ARG cc_start: 0.8328 (ttt90) cc_final: 0.8112 (ttt-90) REVERT: E 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8757 (m-40) REVERT: E 355 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7979 (ptt-90) REVERT: E 395 GLU cc_start: 0.7778 (mp0) cc_final: 0.7555 (mp0) REVERT: E 449 ASP cc_start: 0.7523 (t70) cc_final: 0.7085 (t70) REVERT: F 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 146 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.4605 (pp20) REVERT: F 161 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8323 (mtt180) REVERT: F 224 ARG cc_start: 0.8332 (ttt90) cc_final: 0.8131 (ttt-90) REVERT: F 229 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7964 (ptpp) REVERT: F 312 ASN cc_start: 0.9066 (m-40) cc_final: 0.8781 (m-40) REVERT: F 355 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8042 (ptt-90) REVERT: F 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7527 (mp0) REVERT: G 91 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8629 (mm) REVERT: G 146 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6050 (pp20) REVERT: G 179 MET cc_start: 0.3655 (mtt) cc_final: 0.2840 (mpp) REVERT: G 224 ARG cc_start: 0.8371 (ttt90) cc_final: 0.8134 (ttt-90) REVERT: G 312 ASN cc_start: 0.9079 (m-40) cc_final: 0.8726 (m-40) REVERT: G 355 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: G 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.8154 (mt0) REVERT: G 449 ASP cc_start: 0.7506 (t70) cc_final: 0.7012 (t70) REVERT: H 91 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8616 (mm) REVERT: H 312 ASN cc_start: 0.9092 (m-40) cc_final: 0.8795 (m-40) REVERT: H 355 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8092 (ptt-90) REVERT: H 395 GLU cc_start: 0.7789 (mp0) cc_final: 0.7570 (mp0) REVERT: H 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8206 (mt0) REVERT: H 449 ASP cc_start: 0.7528 (t70) cc_final: 0.7106 (t70) outliers start: 152 outliers final: 108 residues processed: 735 average time/residue: 0.1860 time to fit residues: 215.7631 Evaluate side-chains 689 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 563 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 277 GLN A 303 ASN A 454 GLN A 498 GLN B 112 GLN B 277 GLN B 303 ASN B 498 GLN C 112 GLN C 277 GLN C 303 ASN C 498 GLN D 112 GLN D 277 GLN D 303 ASN D 454 GLN D 498 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 277 GLN E 303 ASN E 498 GLN F 112 GLN F 277 GLN F 303 ASN F 454 GLN F 498 GLN G 112 GLN G 277 GLN G 303 ASN G 498 GLN H 112 GLN H 277 GLN H 303 ASN H 454 GLN H 498 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.153050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106748 restraints weight = 33922.084| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.95 r_work: 0.2855 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30593 Z= 0.150 Angle : 0.560 6.487 41496 Z= 0.296 Chirality : 0.043 0.143 4800 Planarity : 0.004 0.084 5160 Dihedral : 15.743 164.444 5407 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.14 % Allowed : 15.74 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.56 (0.13), residues: 3792 helix: 0.23 (0.14), residues: 1424 sheet: -0.74 (0.26), residues: 272 loop : -2.07 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 203 TYR 0.015 0.001 TYR G 400 PHE 0.016 0.001 PHE E 401 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00338 (30592) covalent geometry : angle 0.56018 (41496) hydrogen bonds : bond 0.03536 ( 1090) hydrogen bonds : angle 5.34607 ( 3078) Misc. bond : bond 0.00221 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 653 time to evaluate : 0.883 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 134 LYS cc_start: 0.7842 (tptt) cc_final: 0.7556 (tppt) REVERT: A 229 LYS cc_start: 0.8083 (ptpp) cc_final: 0.7859 (ptpp) REVERT: A 243 GLN cc_start: 0.8090 (mp10) cc_final: 0.7721 (mp10) REVERT: A 312 ASN cc_start: 0.9253 (m-40) cc_final: 0.9003 (m-40) REVERT: A 449 ASP cc_start: 0.7813 (t70) cc_final: 0.7298 (t70) REVERT: B 91 ILE cc_start: 0.8956 (mm) cc_final: 0.8545 (mm) REVERT: B 134 LYS cc_start: 0.7885 (tptt) cc_final: 0.7552 (tppt) REVERT: B 202 GLN cc_start: 0.8432 (tt0) cc_final: 0.8144 (mm-40) REVERT: B 312 ASN cc_start: 0.9242 (m-40) cc_final: 0.8991 (m-40) REVERT: B 395 GLU cc_start: 0.8130 (mp0) cc_final: 0.7861 (mp0) REVERT: B 411 TYR cc_start: 0.8908 (t80) cc_final: 0.8696 (t80) REVERT: B 412 ARG cc_start: 0.8180 (ptt180) cc_final: 0.7977 (ptt180) REVERT: B 449 ASP cc_start: 0.7893 (t70) cc_final: 0.7232 (t70) REVERT: B 455 LYS cc_start: 0.8146 (ptpp) cc_final: 0.7901 (ptpp) REVERT: C 135 MET cc_start: 0.8282 (mpp) cc_final: 0.7728 (mpp) REVERT: C 202 GLN cc_start: 0.8468 (tt0) cc_final: 0.8069 (mt0) REVERT: C 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8967 (m-40) REVERT: C 400 TYR cc_start: 0.7695 (m-80) cc_final: 0.7234 (m-80) REVERT: C 412 ARG cc_start: 0.8285 (ptt180) cc_final: 0.8078 (ptt180) REVERT: C 449 ASP cc_start: 0.7952 (t0) cc_final: 0.7693 (t70) REVERT: D 134 LYS cc_start: 0.7932 (tptt) cc_final: 0.7688 (tppt) REVERT: D 184 GLU cc_start: 0.2148 (OUTLIER) cc_final: 0.0294 (tp30) REVERT: D 202 GLN cc_start: 0.8434 (tt0) cc_final: 0.8049 (mt0) REVERT: D 312 ASN cc_start: 0.9275 (m-40) cc_final: 0.8990 (m-40) REVERT: D 395 GLU cc_start: 0.8116 (mp0) cc_final: 0.7810 (mp0) REVERT: D 411 TYR cc_start: 0.8872 (t80) cc_final: 0.8567 (t80) REVERT: D 412 ARG cc_start: 0.8236 (ptt180) cc_final: 0.8020 (ptt180) REVERT: D 449 ASP cc_start: 0.7751 (t70) cc_final: 0.7367 (t70) REVERT: E 91 ILE cc_start: 0.8961 (mm) cc_final: 0.8546 (mm) REVERT: E 134 LYS cc_start: 0.7969 (tptt) cc_final: 0.7671 (tppt) REVERT: E 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8981 (m-40) REVERT: E 395 GLU cc_start: 0.8077 (mp0) cc_final: 0.7844 (mp0) REVERT: E 448 GLN cc_start: 0.7587 (tt0) cc_final: 0.7341 (tt0) REVERT: E 449 ASP cc_start: 0.7865 (t70) cc_final: 0.7166 (t70) REVERT: F 243 GLN cc_start: 0.8115 (mp10) cc_final: 0.7220 (mp-120) REVERT: F 312 ASN cc_start: 0.9229 (m-40) cc_final: 0.8971 (m-40) REVERT: F 395 GLU cc_start: 0.8059 (mp0) cc_final: 0.7796 (mp0) REVERT: G 179 MET cc_start: 0.3969 (mtt) cc_final: 0.3237 (mpp) REVERT: G 231 ARG cc_start: 0.8600 (ptp90) cc_final: 0.8364 (mtm110) REVERT: G 312 ASN cc_start: 0.9259 (m-40) cc_final: 0.8965 (m-40) REVERT: G 395 GLU cc_start: 0.8156 (mp0) cc_final: 0.7860 (mp0) REVERT: G 412 ARG cc_start: 0.8252 (ptt180) cc_final: 0.8016 (ptt180) REVERT: H 231 ARG cc_start: 0.8712 (ptp90) cc_final: 0.8477 (mtm180) REVERT: H 312 ASN cc_start: 0.9276 (m-40) cc_final: 0.9031 (m-40) REVERT: H 395 GLU cc_start: 0.8047 (mp0) cc_final: 0.7792 (mp0) REVERT: H 411 TYR cc_start: 0.8861 (t80) cc_final: 0.8559 (t80) REVERT: H 441 GLN cc_start: 0.8491 (mt0) cc_final: 0.8289 (mt0) outliers start: 98 outliers final: 68 residues processed: 731 average time/residue: 0.1882 time to fit residues: 215.7178 Evaluate side-chains 675 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 606 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE 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 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 314 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 14 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 364 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 123 optimal weight: 0.0170 chunk 241 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 334 GLN C 334 GLN D 334 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 334 GLN G 334 GLN H 334 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.154409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.108080 restraints weight = 33854.324| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.95 r_work: 0.2869 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30593 Z= 0.131 Angle : 0.511 7.004 41496 Z= 0.269 Chirality : 0.042 0.136 4800 Planarity : 0.004 0.033 5160 Dihedral : 14.324 164.716 5274 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.98 % Allowed : 17.05 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.84 (0.13), residues: 3792 helix: 0.88 (0.14), residues: 1424 sheet: -0.28 (0.26), residues: 288 loop : -1.71 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.012 0.001 TYR C 294 PHE 0.013 0.001 PHE C 401 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (30592) covalent geometry : angle 0.51059 (41496) hydrogen bonds : bond 0.03258 ( 1090) hydrogen bonds : angle 4.93549 ( 3078) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 617 time to evaluate : 0.950 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: symmetry clash REVERT: A 202 GLN cc_start: 0.8365 (tt0) cc_final: 0.8137 (mm-40) REVERT: A 225 THR cc_start: 0.8343 (m) cc_final: 0.8060 (m) REVERT: A 229 LYS cc_start: 0.8113 (ptpp) cc_final: 0.7871 (ptpp) REVERT: A 243 GLN cc_start: 0.8049 (mp10) cc_final: 0.7813 (mp-120) REVERT: A 312 ASN cc_start: 0.9244 (m-40) cc_final: 0.8982 (m-40) REVERT: B 91 ILE cc_start: 0.8930 (mm) cc_final: 0.8454 (mm) REVERT: B 134 LYS cc_start: 0.7850 (tptt) cc_final: 0.7493 (tppt) REVERT: B 243 GLN cc_start: 0.7767 (mp-120) cc_final: 0.7488 (mp10) REVERT: B 312 ASN cc_start: 0.9215 (m-40) cc_final: 0.8958 (m-40) REVERT: B 395 GLU cc_start: 0.8155 (mp0) cc_final: 0.7892 (mp0) REVERT: B 441 GLN cc_start: 0.8481 (mt0) cc_final: 0.8193 (mt0) REVERT: B 449 ASP cc_start: 0.7774 (t70) cc_final: 0.7335 (t70) REVERT: C 265 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8038 (mm-40) REVERT: C 286 MET cc_start: 0.8859 (tpp) cc_final: 0.8647 (tpp) REVERT: C 312 ASN cc_start: 0.9218 (m-40) cc_final: 0.8943 (m-40) REVERT: C 449 ASP cc_start: 0.7793 (t0) cc_final: 0.7538 (t70) REVERT: D 243 GLN cc_start: 0.7805 (mp-120) cc_final: 0.7178 (mp10) REVERT: D 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8958 (m-40) REVERT: D 395 GLU cc_start: 0.8183 (mp0) cc_final: 0.7897 (mp0) REVERT: D 449 ASP cc_start: 0.7772 (t70) cc_final: 0.7339 (t70) REVERT: D 455 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7745 (ptpp) REVERT: E 91 ILE cc_start: 0.8940 (mm) cc_final: 0.8495 (mm) REVERT: E 134 LYS cc_start: 0.7959 (tptt) cc_final: 0.7645 (tppt) REVERT: E 312 ASN cc_start: 0.9220 (m-40) cc_final: 0.8956 (m-40) REVERT: E 395 GLU cc_start: 0.8133 (mp0) cc_final: 0.7902 (mp0) REVERT: F 206 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7015 (mtmm) REVERT: F 243 GLN cc_start: 0.8106 (mp10) cc_final: 0.7833 (mp-120) REVERT: F 312 ASN cc_start: 0.9210 (m-40) cc_final: 0.8948 (m-40) REVERT: F 395 GLU cc_start: 0.8122 (mp0) cc_final: 0.7859 (mp0) REVERT: F 441 GLN cc_start: 0.8495 (mt0) cc_final: 0.8246 (mt0) REVERT: F 449 ASP cc_start: 0.7613 (t0) cc_final: 0.7120 (t70) REVERT: G 179 MET cc_start: 0.3582 (mtt) cc_final: 0.3068 (mpp) REVERT: G 231 ARG cc_start: 0.8593 (ptp90) cc_final: 0.8367 (mtm110) REVERT: G 286 MET cc_start: 0.8900 (tpp) cc_final: 0.8694 (tpp) REVERT: G 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8907 (m-40) REVERT: G 395 GLU cc_start: 0.8135 (mp0) cc_final: 0.7827 (mp0) REVERT: G 441 GLN cc_start: 0.8477 (mt0) cc_final: 0.8185 (mt0) REVERT: H 202 GLN cc_start: 0.8403 (tt0) cc_final: 0.8087 (mm-40) REVERT: H 225 THR cc_start: 0.8269 (m) cc_final: 0.7790 (p) REVERT: H 231 ARG cc_start: 0.8757 (ptp90) cc_final: 0.8512 (mtm180) REVERT: H 243 GLN cc_start: 0.7847 (mp-120) cc_final: 0.7570 (mp10) REVERT: H 312 ASN cc_start: 0.9261 (m-40) cc_final: 0.9001 (m-40) REVERT: H 395 GLU cc_start: 0.8126 (mp0) cc_final: 0.7902 (mp0) outliers start: 93 outliers final: 83 residues processed: 677 average time/residue: 0.1902 time to fit residues: 202.5555 Evaluate side-chains 681 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 597 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR 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 148 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 358 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.104511 restraints weight = 33997.883| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.86 r_work: 0.2837 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 30593 Z= 0.305 Angle : 0.599 5.898 41496 Z= 0.314 Chirality : 0.046 0.139 4800 Planarity : 0.004 0.040 5160 Dihedral : 14.339 167.569 5261 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.90 % Allowed : 16.79 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.84 (0.14), residues: 3792 helix: 0.85 (0.14), residues: 1432 sheet: -0.19 (0.27), residues: 272 loop : -1.69 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 231 TYR 0.016 0.002 TYR F 348 PHE 0.011 0.001 PHE G 99 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00703 (30592) covalent geometry : angle 0.59862 (41496) hydrogen bonds : bond 0.04042 ( 1090) hydrogen bonds : angle 5.14463 ( 3078) Misc. bond : bond 0.00207 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 601 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: A 134 LYS cc_start: 0.7823 (tptt) cc_final: 0.7619 (tppt) REVERT: A 229 LYS cc_start: 0.8099 (ptpp) cc_final: 0.7813 (ptpp) REVERT: A 243 GLN cc_start: 0.8011 (mp10) cc_final: 0.7731 (mp-120) REVERT: A 312 ASN cc_start: 0.9257 (m-40) cc_final: 0.8936 (m-40) REVERT: A 330 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (pp) REVERT: A 449 ASP cc_start: 0.7890 (t70) cc_final: 0.7337 (t70) REVERT: A 476 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 312 ASN cc_start: 0.9281 (m-40) cc_final: 0.8981 (m-40) REVERT: B 330 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8801 (pp) REVERT: B 395 GLU cc_start: 0.8068 (mp0) cc_final: 0.7685 (mp0) REVERT: B 441 GLN cc_start: 0.8435 (mt0) cc_final: 0.8180 (mt0) REVERT: B 449 ASP cc_start: 0.7915 (t70) cc_final: 0.7397 (t70) REVERT: C 135 MET cc_start: 0.8338 (mpp) cc_final: 0.7903 (mpp) REVERT: C 243 GLN cc_start: 0.7812 (mp10) cc_final: 0.7340 (mp-120) REVERT: C 312 ASN cc_start: 0.9261 (m-40) cc_final: 0.8937 (m-40) REVERT: C 412 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7884 (ptt180) REVERT: C 441 GLN cc_start: 0.8461 (mt0) cc_final: 0.8228 (mt0) REVERT: D 134 LYS cc_start: 0.7888 (tptt) cc_final: 0.7624 (tppt) REVERT: D 184 GLU cc_start: 0.2175 (OUTLIER) cc_final: 0.0173 (tp30) REVERT: D 202 GLN cc_start: 0.8422 (tt0) cc_final: 0.8014 (mt0) REVERT: D 243 GLN cc_start: 0.7820 (mp-120) cc_final: 0.7184 (mp10) REVERT: D 312 ASN cc_start: 0.9280 (m-40) cc_final: 0.8942 (m-40) REVERT: D 330 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8823 (pp) REVERT: D 441 GLN cc_start: 0.8467 (mt0) cc_final: 0.8209 (mt0) REVERT: D 449 ASP cc_start: 0.7907 (t70) cc_final: 0.7470 (t70) REVERT: E 134 LYS cc_start: 0.7903 (tptt) cc_final: 0.7606 (tppt) REVERT: E 243 GLN cc_start: 0.7906 (mp-120) cc_final: 0.7687 (mp10) REVERT: E 312 ASN cc_start: 0.9264 (m-40) cc_final: 0.8945 (m-40) REVERT: E 330 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8809 (pp) REVERT: E 395 GLU cc_start: 0.8089 (mp0) cc_final: 0.7765 (mp0) REVERT: E 441 GLN cc_start: 0.8434 (mt0) cc_final: 0.8179 (mt0) REVERT: F 184 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.4121 (tp30) REVERT: F 231 ARG cc_start: 0.8269 (mtm110) cc_final: 0.7940 (mtm180) REVERT: F 243 GLN cc_start: 0.8069 (mp10) cc_final: 0.7762 (mp-120) REVERT: F 265 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7984 (mm-40) REVERT: F 312 ASN cc_start: 0.9262 (m-40) cc_final: 0.8930 (m-40) REVERT: F 330 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8771 (pp) REVERT: F 395 GLU cc_start: 0.8059 (mp0) cc_final: 0.7720 (mp0) REVERT: F 412 ARG cc_start: 0.8151 (ptt180) cc_final: 0.7883 (ptt180) REVERT: F 441 GLN cc_start: 0.8438 (mt0) cc_final: 0.8150 (mt0) REVERT: F 476 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8970 (mp) REVERT: G 135 MET cc_start: 0.8171 (mpp) cc_final: 0.7574 (mpp) REVERT: G 179 MET cc_start: 0.3648 (mtt) cc_final: 0.2814 (mpp) REVERT: G 243 GLN cc_start: 0.7818 (mp10) cc_final: 0.7355 (mp-120) REVERT: G 312 ASN cc_start: 0.9252 (m-40) cc_final: 0.8875 (m-40) REVERT: G 330 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8812 (pp) REVERT: G 395 GLU cc_start: 0.8100 (mp0) cc_final: 0.7707 (mp0) REVERT: G 412 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7915 (ptt180) REVERT: G 441 GLN cc_start: 0.8451 (mt0) cc_final: 0.8201 (mt0) REVERT: G 449 ASP cc_start: 0.7926 (t70) cc_final: 0.7440 (t70) REVERT: G 455 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7757 (ptpp) REVERT: H 182 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6675 (mmm160) REVERT: H 225 THR cc_start: 0.8124 (m) cc_final: 0.7685 (p) REVERT: H 231 ARG cc_start: 0.8733 (ptp90) cc_final: 0.8439 (mtm180) REVERT: H 312 ASN cc_start: 0.9281 (m-40) cc_final: 0.8953 (m-40) REVERT: H 330 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8793 (pp) REVERT: H 395 GLU cc_start: 0.8083 (mp0) cc_final: 0.7775 (mp0) REVERT: H 441 GLN cc_start: 0.8390 (mt0) cc_final: 0.8161 (mt0) REVERT: H 449 ASP cc_start: 0.7880 (t70) cc_final: 0.7253 (t0) outliers start: 153 outliers final: 125 residues processed: 707 average time/residue: 0.1860 time to fit residues: 207.9867 Evaluate side-chains 721 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 585 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE 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 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR 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 82 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 321 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.152462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105211 restraints weight = 33827.554| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.97 r_work: 0.2875 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30593 Z= 0.135 Angle : 0.507 5.701 41496 Z= 0.268 Chirality : 0.042 0.157 4800 Planarity : 0.004 0.045 5160 Dihedral : 13.840 171.261 5261 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.71 % Allowed : 18.04 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.57 (0.14), residues: 3792 helix: 0.90 (0.14), residues: 1480 sheet: 0.09 (0.27), residues: 272 loop : -1.47 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 231 TYR 0.012 0.001 TYR F 353 PHE 0.007 0.001 PHE C 24 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00305 (30592) covalent geometry : angle 0.50746 (41496) hydrogen bonds : bond 0.03117 ( 1090) hydrogen bonds : angle 4.85121 ( 3078) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 611 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: symmetry clash REVERT: A 202 GLN cc_start: 0.8367 (tt0) cc_final: 0.8006 (mm-40) REVERT: A 225 THR cc_start: 0.8304 (m) cc_final: 0.8004 (m) REVERT: A 229 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7779 (ptpp) REVERT: A 243 GLN cc_start: 0.8072 (mp10) cc_final: 0.7273 (mp10) REVERT: A 312 ASN cc_start: 0.9254 (m-40) cc_final: 0.8956 (m-40) REVERT: A 400 TYR cc_start: 0.7657 (m-80) cc_final: 0.6939 (m-80) REVERT: A 449 ASP cc_start: 0.7884 (t70) cc_final: 0.7327 (t70) REVERT: B 78 MET cc_start: 0.8977 (tpp) cc_final: 0.8639 (tpp) REVERT: B 134 LYS cc_start: 0.7930 (tptt) cc_final: 0.7707 (tppt) REVERT: B 243 GLN cc_start: 0.7859 (mp-120) cc_final: 0.7651 (mp10) REVERT: B 312 ASN cc_start: 0.9247 (m-40) cc_final: 0.8974 (m-40) REVERT: B 395 GLU cc_start: 0.8131 (mp0) cc_final: 0.7770 (mp0) REVERT: B 441 GLN cc_start: 0.8432 (mt0) cc_final: 0.8164 (mt0) REVERT: B 449 ASP cc_start: 0.7928 (t70) cc_final: 0.7334 (t70) REVERT: C 243 GLN cc_start: 0.7731 (mp10) cc_final: 0.7477 (mp10) REVERT: C 286 MET cc_start: 0.8882 (tpp) cc_final: 0.8647 (tpp) REVERT: C 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8927 (m-40) REVERT: C 441 GLN cc_start: 0.8398 (mt0) cc_final: 0.8166 (mt0) REVERT: C 449 ASP cc_start: 0.7563 (t0) cc_final: 0.7290 (t70) REVERT: D 184 GLU cc_start: 0.2122 (OUTLIER) cc_final: 0.0278 (tp30) REVERT: D 243 GLN cc_start: 0.7805 (mp-120) cc_final: 0.7125 (mp-120) REVERT: D 312 ASN cc_start: 0.9244 (m-40) cc_final: 0.8946 (m-40) REVERT: D 395 GLU cc_start: 0.8157 (mp0) cc_final: 0.7859 (mp0) REVERT: D 441 GLN cc_start: 0.8450 (mt0) cc_final: 0.8186 (mt0) REVERT: D 449 ASP cc_start: 0.7905 (t70) cc_final: 0.7451 (t70) REVERT: E 225 THR cc_start: 0.8346 (m) cc_final: 0.7878 (p) REVERT: E 243 GLN cc_start: 0.7951 (mp-120) cc_final: 0.7673 (mp-120) REVERT: E 286 MET cc_start: 0.8898 (tpp) cc_final: 0.8675 (tpp) REVERT: E 312 ASN cc_start: 0.9258 (m-40) cc_final: 0.8978 (m-40) REVERT: E 395 GLU cc_start: 0.8124 (mp0) cc_final: 0.7859 (mp0) REVERT: E 441 GLN cc_start: 0.8418 (mt0) cc_final: 0.8148 (mt0) REVERT: E 448 GLN cc_start: 0.7583 (tt0) cc_final: 0.7339 (tt0) REVERT: F 231 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7966 (mtm180) REVERT: F 243 GLN cc_start: 0.8080 (mp10) cc_final: 0.7222 (mp10) REVERT: F 312 ASN cc_start: 0.9232 (m-40) cc_final: 0.8932 (m-40) REVERT: F 395 GLU cc_start: 0.8105 (mp0) cc_final: 0.7790 (mp0) REVERT: F 412 ARG cc_start: 0.8126 (ptt180) cc_final: 0.7858 (ptt180) REVERT: F 441 GLN cc_start: 0.8460 (mt0) cc_final: 0.8178 (mt0) REVERT: F 449 ASP cc_start: 0.7536 (t0) cc_final: 0.7150 (t70) REVERT: G 135 MET cc_start: 0.8268 (mpp) cc_final: 0.7824 (mpp) REVERT: G 179 MET cc_start: 0.3772 (mtt) cc_final: 0.3080 (mpp) REVERT: G 243 GLN cc_start: 0.7871 (mp10) cc_final: 0.7338 (mp-120) REVERT: G 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8919 (m-40) REVERT: G 395 GLU cc_start: 0.8149 (mp0) cc_final: 0.7818 (mp0) REVERT: G 441 GLN cc_start: 0.8425 (mt0) cc_final: 0.8156 (mt0) REVERT: G 449 ASP cc_start: 0.7916 (t70) cc_final: 0.7423 (t70) REVERT: G 455 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7813 (ptpp) REVERT: H 139 PHE cc_start: 0.8820 (p90) cc_final: 0.8612 (p90) REVERT: H 202 GLN cc_start: 0.8352 (tt0) cc_final: 0.8085 (mm-40) REVERT: H 231 ARG cc_start: 0.8749 (ptp90) cc_final: 0.8471 (mtm180) REVERT: H 243 GLN cc_start: 0.7877 (mp-120) cc_final: 0.7672 (mp10) REVERT: H 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8948 (m-40) REVERT: H 395 GLU cc_start: 0.8100 (mp0) cc_final: 0.7831 (mp0) REVERT: H 449 ASP cc_start: 0.7909 (t70) cc_final: 0.7332 (t70) outliers start: 147 outliers final: 115 residues processed: 718 average time/residue: 0.1861 time to fit residues: 211.8277 Evaluate side-chains 717 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 601 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 0.0270 chunk 303 optimal weight: 2.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108973 restraints weight = 33639.856| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.95 r_work: 0.2882 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30593 Z= 0.133 Angle : 0.502 5.388 41496 Z= 0.266 Chirality : 0.042 0.143 4800 Planarity : 0.004 0.044 5160 Dihedral : 13.575 178.988 5259 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.26 % Allowed : 18.81 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.37 (0.14), residues: 3792 helix: 1.06 (0.14), residues: 1472 sheet: 0.18 (0.27), residues: 272 loop : -1.33 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 231 TYR 0.013 0.001 TYR G 400 PHE 0.014 0.001 PHE A 401 HIS 0.002 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00301 (30592) covalent geometry : angle 0.50204 (41496) hydrogen bonds : bond 0.03058 ( 1090) hydrogen bonds : angle 4.75605 ( 3078) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 603 time to evaluate : 1.051 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: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7827 (tptt) cc_final: 0.7592 (tppt) REVERT: A 179 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4196 (mtm) REVERT: A 202 GLN cc_start: 0.8361 (tt0) cc_final: 0.8121 (mm-40) REVERT: A 225 THR cc_start: 0.8291 (m) cc_final: 0.7984 (m) REVERT: A 229 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7858 (ptpp) REVERT: A 243 GLN cc_start: 0.8053 (mp10) cc_final: 0.7270 (mp10) REVERT: A 312 ASN cc_start: 0.9236 (m-40) cc_final: 0.8959 (m-40) REVERT: A 400 TYR cc_start: 0.7644 (m-80) cc_final: 0.6929 (m-80) REVERT: A 449 ASP cc_start: 0.7893 (t70) cc_final: 0.7318 (t70) REVERT: A 470 ASP cc_start: 0.8972 (m-30) cc_final: 0.8724 (m-30) REVERT: B 134 LYS cc_start: 0.7839 (tptt) cc_final: 0.7544 (tppt) REVERT: B 206 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7502 (mttm) REVERT: B 243 GLN cc_start: 0.7883 (mp-120) cc_final: 0.7650 (mp10) REVERT: B 286 MET cc_start: 0.8933 (tpp) cc_final: 0.8708 (tpp) REVERT: B 312 ASN cc_start: 0.9238 (m-40) cc_final: 0.8960 (m-40) REVERT: B 395 GLU cc_start: 0.8127 (mp0) cc_final: 0.7815 (mp0) REVERT: B 441 GLN cc_start: 0.8415 (mt0) cc_final: 0.8161 (mt0) REVERT: B 449 ASP cc_start: 0.7904 (t70) cc_final: 0.7401 (t70) REVERT: C 184 GLU cc_start: 0.4862 (OUTLIER) cc_final: 0.4251 (tp30) REVERT: C 225 THR cc_start: 0.7990 (m) cc_final: 0.7563 (p) REVERT: C 243 GLN cc_start: 0.7731 (mp10) cc_final: 0.7340 (mp10) REVERT: C 286 MET cc_start: 0.8878 (tpp) cc_final: 0.8639 (tpp) REVERT: C 312 ASN cc_start: 0.9226 (m-40) cc_final: 0.8921 (m-40) REVERT: C 441 GLN cc_start: 0.8379 (mt0) cc_final: 0.8136 (mt0) REVERT: C 449 ASP cc_start: 0.7580 (t0) cc_final: 0.7311 (t70) REVERT: D 134 LYS cc_start: 0.7888 (tppt) cc_final: 0.7628 (tppt) REVERT: D 184 GLU cc_start: 0.2319 (OUTLIER) cc_final: 0.0491 (tp30) REVERT: D 243 GLN cc_start: 0.7784 (mp-120) cc_final: 0.7110 (mp-120) REVERT: D 286 MET cc_start: 0.8929 (tpp) cc_final: 0.8697 (tpp) REVERT: D 312 ASN cc_start: 0.9226 (m-40) cc_final: 0.8922 (m-40) REVERT: D 395 GLU cc_start: 0.8129 (mp0) cc_final: 0.7836 (mp0) REVERT: D 441 GLN cc_start: 0.8414 (mt0) cc_final: 0.8163 (mt0) REVERT: D 449 ASP cc_start: 0.7938 (t70) cc_final: 0.7436 (t70) REVERT: E 134 LYS cc_start: 0.7894 (tppt) cc_final: 0.7572 (tppt) REVERT: E 202 GLN cc_start: 0.8378 (tt0) cc_final: 0.8130 (mm-40) REVERT: E 206 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7608 (mttm) REVERT: E 225 THR cc_start: 0.8363 (m) cc_final: 0.7912 (p) REVERT: E 243 GLN cc_start: 0.7951 (mp-120) cc_final: 0.7638 (mp-120) REVERT: E 286 MET cc_start: 0.8909 (tpp) cc_final: 0.8674 (tpp) REVERT: E 312 ASN cc_start: 0.9244 (m-40) cc_final: 0.8950 (m-40) REVERT: E 395 GLU cc_start: 0.8151 (mp0) cc_final: 0.7904 (mp0) REVERT: E 448 GLN cc_start: 0.7628 (tt0) cc_final: 0.7376 (tt0) REVERT: F 206 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7202 (mtmm) REVERT: F 231 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8001 (mtm180) REVERT: F 243 GLN cc_start: 0.8080 (mp10) cc_final: 0.7235 (mp10) REVERT: F 312 ASN cc_start: 0.9229 (m-40) cc_final: 0.8916 (m-40) REVERT: F 395 GLU cc_start: 0.8131 (mp0) cc_final: 0.7847 (mp0) REVERT: F 412 ARG cc_start: 0.8047 (ptt180) cc_final: 0.7789 (ptt180) REVERT: F 441 GLN cc_start: 0.8420 (mt0) cc_final: 0.8131 (mt0) REVERT: F 449 ASP cc_start: 0.7603 (t0) cc_final: 0.7304 (t70) REVERT: G 114 PHE cc_start: 0.8281 (m-10) cc_final: 0.8079 (m-10) REVERT: G 135 MET cc_start: 0.8328 (mpp) cc_final: 0.7896 (mpp) REVERT: G 179 MET cc_start: 0.3813 (mtt) cc_final: 0.3174 (mpp) REVERT: G 243 GLN cc_start: 0.7869 (mp10) cc_final: 0.7151 (mp10) REVERT: G 312 ASN cc_start: 0.9222 (m-40) cc_final: 0.8903 (m-40) REVERT: G 395 GLU cc_start: 0.8163 (mp0) cc_final: 0.7853 (mp0) REVERT: G 441 GLN cc_start: 0.8392 (mt0) cc_final: 0.8132 (mt0) REVERT: G 449 ASP cc_start: 0.7881 (t70) cc_final: 0.7474 (t70) REVERT: G 455 LYS cc_start: 0.8006 (ptpp) cc_final: 0.7797 (ptpp) REVERT: H 202 GLN cc_start: 0.8355 (tt0) cc_final: 0.8054 (mm-40) REVERT: H 206 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7548 (mttm) REVERT: H 231 ARG cc_start: 0.8784 (ptp90) cc_final: 0.8498 (mtm180) REVERT: H 243 GLN cc_start: 0.7898 (mp-120) cc_final: 0.7661 (mp10) REVERT: H 286 MET cc_start: 0.8921 (tpp) cc_final: 0.8714 (tpp) REVERT: H 312 ASN cc_start: 0.9232 (m-40) cc_final: 0.8954 (m-40) REVERT: H 337 MET cc_start: 0.8752 (mmm) cc_final: 0.8338 (mtt) REVERT: H 395 GLU cc_start: 0.8117 (mp0) cc_final: 0.7872 (mp0) REVERT: H 449 ASP cc_start: 0.7935 (t70) cc_final: 0.7353 (t70) outliers start: 133 outliers final: 109 residues processed: 699 average time/residue: 0.1848 time to fit residues: 204.3101 Evaluate side-chains 714 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 598 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 292 optimal weight: 4.9990 chunk 343 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 282 optimal weight: 0.0010 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 380 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106625 restraints weight = 33652.660| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.95 r_work: 0.2848 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 30593 Z= 0.202 Angle : 0.542 6.332 41496 Z= 0.286 Chirality : 0.044 0.148 4800 Planarity : 0.004 0.038 5160 Dihedral : 13.484 168.482 5255 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.42 % Allowed : 19.26 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.57 (0.14), residues: 3792 helix: 0.96 (0.14), residues: 1480 sheet: -0.66 (0.25), residues: 352 loop : -1.41 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 412 TYR 0.013 0.002 TYR G 400 PHE 0.007 0.001 PHE H 99 HIS 0.003 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00463 (30592) covalent geometry : angle 0.54179 (41496) hydrogen bonds : bond 0.03439 ( 1090) hydrogen bonds : angle 4.86096 ( 3078) Misc. bond : bond 0.00140 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 605 time to evaluate : 1.054 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 134 LYS cc_start: 0.7817 (tptt) cc_final: 0.7584 (tppt) REVERT: A 202 GLN cc_start: 0.8420 (tt0) cc_final: 0.8200 (mm-40) REVERT: A 225 THR cc_start: 0.8281 (m) cc_final: 0.8043 (m) REVERT: A 243 GLN cc_start: 0.8041 (mp10) cc_final: 0.7253 (mp10) REVERT: A 265 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7951 (mm-40) REVERT: A 312 ASN cc_start: 0.9267 (m-40) cc_final: 0.8940 (m-40) REVERT: A 449 ASP cc_start: 0.7957 (t70) cc_final: 0.7624 (t0) REVERT: A 476 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9010 (mp) REVERT: B 134 LYS cc_start: 0.7829 (tptt) cc_final: 0.7558 (tppt) REVERT: B 206 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7606 (mttm) REVERT: B 243 GLN cc_start: 0.7888 (mp-120) cc_final: 0.7601 (mp-120) REVERT: B 265 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 312 ASN cc_start: 0.9270 (m-40) cc_final: 0.8981 (m-40) REVERT: B 395 GLU cc_start: 0.8143 (mp0) cc_final: 0.7823 (mp0) REVERT: B 441 GLN cc_start: 0.8396 (mt0) cc_final: 0.8154 (mt0) REVERT: C 135 MET cc_start: 0.8305 (mpp) cc_final: 0.7923 (mpp) REVERT: C 184 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4306 (tp30) REVERT: C 225 THR cc_start: 0.8040 (m) cc_final: 0.7600 (p) REVERT: C 243 GLN cc_start: 0.7727 (mp10) cc_final: 0.7309 (mp10) REVERT: C 286 MET cc_start: 0.8919 (tpp) cc_final: 0.8690 (tpp) REVERT: C 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8927 (m-40) REVERT: C 441 GLN cc_start: 0.8364 (mt0) cc_final: 0.8136 (mt0) REVERT: C 449 ASP cc_start: 0.7599 (t0) cc_final: 0.7338 (t70) REVERT: D 134 LYS cc_start: 0.7803 (tppt) cc_final: 0.7554 (tppt) REVERT: D 184 GLU cc_start: 0.2366 (OUTLIER) cc_final: 0.0468 (tp30) REVERT: D 243 GLN cc_start: 0.7883 (mp-120) cc_final: 0.7211 (mp-120) REVERT: D 312 ASN cc_start: 0.9268 (m-40) cc_final: 0.8929 (m-40) REVERT: D 395 GLU cc_start: 0.8128 (mp0) cc_final: 0.7801 (mp0) REVERT: D 421 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6929 (pt0) REVERT: D 441 GLN cc_start: 0.8400 (mt0) cc_final: 0.8166 (mt0) REVERT: D 449 ASP cc_start: 0.7921 (t70) cc_final: 0.7486 (t70) REVERT: D 455 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7817 (ptpp) REVERT: E 21 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: E 134 LYS cc_start: 0.7830 (tppt) cc_final: 0.7558 (tppt) REVERT: E 206 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7578 (mttm) REVERT: E 225 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7917 (p) REVERT: E 286 MET cc_start: 0.8930 (tpp) cc_final: 0.8710 (tpp) REVERT: E 312 ASN cc_start: 0.9275 (m-40) cc_final: 0.8963 (m-40) REVERT: E 395 GLU cc_start: 0.8145 (mp0) cc_final: 0.7882 (mp0) REVERT: E 448 GLN cc_start: 0.7619 (tt0) cc_final: 0.7382 (tt0) REVERT: F 184 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4214 (tp30) REVERT: F 206 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7168 (mtmm) REVERT: F 231 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7954 (mtm180) REVERT: F 243 GLN cc_start: 0.8068 (mp10) cc_final: 0.7815 (mp10) REVERT: F 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8926 (m-40) REVERT: F 395 GLU cc_start: 0.8133 (mp0) cc_final: 0.7808 (mp0) REVERT: F 412 ARG cc_start: 0.8124 (ptt180) cc_final: 0.7857 (ptt180) REVERT: F 441 GLN cc_start: 0.8391 (mt0) cc_final: 0.8130 (mt0) REVERT: F 449 ASP cc_start: 0.7612 (t0) cc_final: 0.7345 (t70) REVERT: F 476 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8982 (mp) REVERT: G 135 MET cc_start: 0.8376 (mpp) cc_final: 0.7919 (mpp) REVERT: G 179 MET cc_start: 0.3888 (mtt) cc_final: 0.3203 (mpp) REVERT: G 206 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7658 (mttm) REVERT: G 243 GLN cc_start: 0.7870 (mp10) cc_final: 0.7471 (mp10) REVERT: G 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8893 (m-40) REVERT: G 395 GLU cc_start: 0.8170 (mp0) cc_final: 0.7827 (mp0) REVERT: G 441 GLN cc_start: 0.8372 (mt0) cc_final: 0.8138 (mt0) REVERT: G 449 ASP cc_start: 0.7909 (t70) cc_final: 0.7484 (t70) REVERT: H 206 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7406 (mttm) REVERT: H 225 THR cc_start: 0.8078 (m) cc_final: 0.7656 (p) REVERT: H 231 ARG cc_start: 0.8763 (ptp90) cc_final: 0.8485 (mtm180) REVERT: H 243 GLN cc_start: 0.7911 (mp-120) cc_final: 0.7622 (mp-120) REVERT: H 312 ASN cc_start: 0.9277 (m-40) cc_final: 0.8946 (m-40) REVERT: H 337 MET cc_start: 0.8854 (mmm) cc_final: 0.8355 (mtt) REVERT: H 395 GLU cc_start: 0.8128 (mp0) cc_final: 0.7877 (mp0) REVERT: H 449 ASP cc_start: 0.7959 (t70) cc_final: 0.7392 (t70) outliers start: 138 outliers final: 111 residues processed: 704 average time/residue: 0.1885 time to fit residues: 210.4057 Evaluate side-chains 705 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 582 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 137 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 334 optimal weight: 0.6980 chunk 305 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 344 optimal weight: 0.9980 chunk 343 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 317 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.155433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.108477 restraints weight = 33731.351| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.95 r_work: 0.2884 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30593 Z= 0.139 Angle : 0.508 6.232 41496 Z= 0.268 Chirality : 0.042 0.153 4800 Planarity : 0.004 0.037 5160 Dihedral : 13.112 145.326 5251 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.85 % Allowed : 20.22 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.28 (0.14), residues: 3792 helix: 1.06 (0.14), residues: 1480 sheet: 0.24 (0.27), residues: 272 loop : -1.23 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 412 TYR 0.012 0.001 TYR F 353 PHE 0.015 0.001 PHE G 401 HIS 0.002 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00315 (30592) covalent geometry : angle 0.50763 (41496) hydrogen bonds : bond 0.03035 ( 1090) hydrogen bonds : angle 4.73262 ( 3078) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 615 time to evaluate : 1.114 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: symmetry clash REVERT: A 78 MET cc_start: 0.8996 (tpp) cc_final: 0.8516 (tpp) REVERT: A 134 LYS cc_start: 0.7778 (tptt) cc_final: 0.7549 (tppt) REVERT: A 202 GLN cc_start: 0.8390 (tt0) cc_final: 0.8144 (mm-40) REVERT: A 243 GLN cc_start: 0.8046 (mp10) cc_final: 0.7268 (mp10) REVERT: A 286 MET cc_start: 0.8899 (tpp) cc_final: 0.8640 (tpp) REVERT: A 312 ASN cc_start: 0.9233 (m-40) cc_final: 0.8930 (m-40) REVERT: A 337 MET cc_start: 0.8909 (mmm) cc_final: 0.8420 (mtt) REVERT: A 441 GLN cc_start: 0.8283 (mt0) cc_final: 0.7896 (mt0) REVERT: A 449 ASP cc_start: 0.7875 (t70) cc_final: 0.7394 (t70) REVERT: A 470 ASP cc_start: 0.8966 (m-30) cc_final: 0.8701 (m-30) REVERT: B 134 LYS cc_start: 0.7773 (tptt) cc_final: 0.7518 (tppt) REVERT: B 205 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8533 (mmtp) REVERT: B 206 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7652 (mttm) REVERT: B 243 GLN cc_start: 0.7879 (mp-120) cc_final: 0.7582 (mp-120) REVERT: B 312 ASN cc_start: 0.9248 (m-40) cc_final: 0.8961 (m-40) REVERT: B 395 GLU cc_start: 0.8139 (mp0) cc_final: 0.7832 (mp0) REVERT: B 441 GLN cc_start: 0.8373 (mt0) cc_final: 0.8125 (mt0) REVERT: C 135 MET cc_start: 0.8263 (mpp) cc_final: 0.7867 (mpp) REVERT: C 205 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8632 (mmtp) REVERT: C 225 THR cc_start: 0.8017 (m) cc_final: 0.7593 (p) REVERT: C 243 GLN cc_start: 0.7731 (mp10) cc_final: 0.6982 (mp10) REVERT: C 286 MET cc_start: 0.8885 (tpp) cc_final: 0.8620 (tpp) REVERT: C 312 ASN cc_start: 0.9241 (m-40) cc_final: 0.8950 (m-40) REVERT: C 449 ASP cc_start: 0.7614 (t0) cc_final: 0.7389 (t70) REVERT: D 134 LYS cc_start: 0.7813 (tppt) cc_final: 0.7607 (tppt) REVERT: D 206 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7594 (mttm) REVERT: D 243 GLN cc_start: 0.7781 (mp-120) cc_final: 0.7103 (mp-120) REVERT: D 286 MET cc_start: 0.8952 (tpp) cc_final: 0.8703 (tpp) REVERT: D 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8945 (m-40) REVERT: D 395 GLU cc_start: 0.8156 (mp0) cc_final: 0.7846 (mp0) REVERT: D 420 MET cc_start: 0.6974 (mtt) cc_final: 0.6667 (mtt) REVERT: D 421 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7091 (pt0) REVERT: D 441 GLN cc_start: 0.8357 (mt0) cc_final: 0.8120 (mt0) REVERT: D 449 ASP cc_start: 0.7943 (t70) cc_final: 0.7497 (t70) REVERT: E 134 LYS cc_start: 0.7793 (tppt) cc_final: 0.7533 (tppt) REVERT: E 205 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8279 (mmtp) REVERT: E 206 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7615 (mttm) REVERT: E 225 THR cc_start: 0.8375 (m) cc_final: 0.7945 (p) REVERT: E 243 GLN cc_start: 0.7946 (mp-120) cc_final: 0.7635 (mp-120) REVERT: E 286 MET cc_start: 0.8938 (tpp) cc_final: 0.8679 (tpp) REVERT: E 312 ASN cc_start: 0.9257 (m-40) cc_final: 0.8960 (m-40) REVERT: E 395 GLU cc_start: 0.8133 (mp0) cc_final: 0.7876 (mp0) REVERT: E 448 GLN cc_start: 0.7653 (tt0) cc_final: 0.7413 (tt0) REVERT: F 184 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4384 (tp30) REVERT: F 202 GLN cc_start: 0.8374 (tt0) cc_final: 0.8092 (mm-40) REVERT: F 231 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7949 (mtm180) REVERT: F 243 GLN cc_start: 0.8066 (mp10) cc_final: 0.7805 (mp10) REVERT: F 312 ASN cc_start: 0.9227 (m-40) cc_final: 0.8923 (m-40) REVERT: F 395 GLU cc_start: 0.8156 (mp0) cc_final: 0.7862 (mp0) REVERT: F 412 ARG cc_start: 0.8070 (ptt180) cc_final: 0.7816 (ptt180) REVERT: F 441 GLN cc_start: 0.8365 (mt0) cc_final: 0.8093 (mt0) REVERT: F 449 ASP cc_start: 0.7600 (t0) cc_final: 0.7382 (t70) REVERT: G 135 MET cc_start: 0.8364 (mpp) cc_final: 0.7895 (mpp) REVERT: G 179 MET cc_start: 0.3785 (mtt) cc_final: 0.3245 (mpp) REVERT: G 206 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7552 (mttm) REVERT: G 243 GLN cc_start: 0.7805 (mp10) cc_final: 0.7037 (mp10) REVERT: G 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8928 (m-40) REVERT: G 395 GLU cc_start: 0.8182 (mp0) cc_final: 0.7871 (mp0) REVERT: G 449 ASP cc_start: 0.7924 (t70) cc_final: 0.7459 (t70) REVERT: G 470 ASP cc_start: 0.8966 (m-30) cc_final: 0.8717 (m-30) REVERT: H 206 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7235 (mttm) REVERT: H 225 THR cc_start: 0.8043 (m) cc_final: 0.7615 (p) REVERT: H 231 ARG cc_start: 0.8771 (ptp90) cc_final: 0.8492 (mtm180) REVERT: H 243 GLN cc_start: 0.7916 (mp-120) cc_final: 0.7153 (mp-120) REVERT: H 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8946 (m-40) REVERT: H 395 GLU cc_start: 0.8130 (mp0) cc_final: 0.7878 (mp0) REVERT: H 449 ASP cc_start: 0.7958 (t70) cc_final: 0.7298 (t70) outliers start: 120 outliers final: 110 residues processed: 704 average time/residue: 0.1856 time to fit residues: 206.5524 Evaluate side-chains 720 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 604 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE 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 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 164 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 377 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 363 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 202 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.155350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.108343 restraints weight = 33552.122| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.94 r_work: 0.2879 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30593 Z= 0.145 Angle : 0.514 6.065 41496 Z= 0.271 Chirality : 0.042 0.149 4800 Planarity : 0.004 0.035 5160 Dihedral : 12.908 113.362 5251 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.20 % Allowed : 19.74 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.39 (0.14), residues: 3792 helix: 1.07 (0.14), residues: 1480 sheet: -0.52 (0.25), residues: 352 loop : -1.28 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 412 TYR 0.011 0.001 TYR H 353 PHE 0.014 0.001 PHE F 401 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00329 (30592) covalent geometry : angle 0.51360 (41496) hydrogen bonds : bond 0.03094 ( 1090) hydrogen bonds : angle 4.71157 ( 3078) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 613 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7738 (tptt) cc_final: 0.7513 (tppt) REVERT: A 202 GLN cc_start: 0.8396 (tt0) cc_final: 0.8153 (mm-40) REVERT: A 206 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7635 (mttm) REVERT: A 225 THR cc_start: 0.8173 (m) cc_final: 0.7714 (p) REVERT: A 243 GLN cc_start: 0.8043 (mp10) cc_final: 0.7262 (mp10) REVERT: A 286 MET cc_start: 0.8892 (tpp) cc_final: 0.8644 (tpp) REVERT: A 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8948 (m-40) REVERT: A 337 MET cc_start: 0.8874 (mmm) cc_final: 0.8413 (mtt) REVERT: A 420 MET cc_start: 0.6845 (mtt) cc_final: 0.6433 (mtt) REVERT: A 441 GLN cc_start: 0.8226 (mt0) cc_final: 0.7860 (mt0) REVERT: A 449 ASP cc_start: 0.7889 (t70) cc_final: 0.7399 (t70) REVERT: A 470 ASP cc_start: 0.8974 (m-30) cc_final: 0.8704 (m-30) REVERT: A 476 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9032 (mt) REVERT: B 205 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8269 (mttm) REVERT: B 206 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7385 (mttm) REVERT: B 243 GLN cc_start: 0.7877 (mp-120) cc_final: 0.7567 (mp-120) REVERT: B 312 ASN cc_start: 0.9252 (m-40) cc_final: 0.8966 (m-40) REVERT: B 395 GLU cc_start: 0.8142 (mp0) cc_final: 0.7828 (mp0) REVERT: C 135 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7858 (mpp) REVERT: C 184 GLU cc_start: 0.5109 (OUTLIER) cc_final: 0.4378 (tp30) REVERT: C 225 THR cc_start: 0.7998 (m) cc_final: 0.7588 (p) REVERT: C 243 GLN cc_start: 0.7729 (mp10) cc_final: 0.7004 (mp10) REVERT: C 286 MET cc_start: 0.8904 (tpp) cc_final: 0.8635 (tpp) REVERT: C 312 ASN cc_start: 0.9233 (m-40) cc_final: 0.8919 (m-40) REVERT: C 449 ASP cc_start: 0.7615 (t0) cc_final: 0.7363 (t70) REVERT: D 114 PHE cc_start: 0.8305 (m-10) cc_final: 0.8082 (m-10) REVERT: D 184 GLU cc_start: 0.2458 (OUTLIER) cc_final: 0.1289 (tp30) REVERT: D 243 GLN cc_start: 0.7781 (mp-120) cc_final: 0.7118 (mp-120) REVERT: D 286 MET cc_start: 0.8949 (tpp) cc_final: 0.8702 (tpp) REVERT: D 312 ASN cc_start: 0.9239 (m-40) cc_final: 0.8951 (m-40) REVERT: D 395 GLU cc_start: 0.8153 (mp0) cc_final: 0.7844 (mp0) REVERT: D 412 ARG cc_start: 0.7965 (ptt180) cc_final: 0.7754 (ptt180) REVERT: D 421 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7102 (pt0) REVERT: D 449 ASP cc_start: 0.7928 (t70) cc_final: 0.7493 (t70) REVERT: E 134 LYS cc_start: 0.7790 (tppt) cc_final: 0.7506 (tppt) REVERT: E 205 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8357 (mmtp) REVERT: E 206 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7627 (mttm) REVERT: E 225 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7810 (p) REVERT: E 286 MET cc_start: 0.8932 (tpp) cc_final: 0.8692 (tpp) REVERT: E 312 ASN cc_start: 0.9258 (m-40) cc_final: 0.8964 (m-40) REVERT: E 395 GLU cc_start: 0.8139 (mp0) cc_final: 0.7881 (mp0) REVERT: E 448 GLN cc_start: 0.7667 (tt0) cc_final: 0.7432 (tt0) REVERT: F 184 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.4404 (tp30) REVERT: F 202 GLN cc_start: 0.8353 (tt0) cc_final: 0.8084 (mm-40) REVERT: F 206 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7147 (mtmm) REVERT: F 231 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7929 (mtm180) REVERT: F 243 GLN cc_start: 0.8066 (mp10) cc_final: 0.7805 (mp10) REVERT: F 312 ASN cc_start: 0.9230 (m-40) cc_final: 0.8902 (m-40) REVERT: F 395 GLU cc_start: 0.8162 (mp0) cc_final: 0.7867 (mp0) REVERT: F 412 ARG cc_start: 0.8065 (ptt180) cc_final: 0.7820 (ptt180) REVERT: F 449 ASP cc_start: 0.7621 (t0) cc_final: 0.7409 (t70) REVERT: F 476 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9033 (mt) REVERT: G 179 MET cc_start: 0.3951 (mtt) cc_final: 0.3152 (mpp) REVERT: G 206 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7426 (mttm) REVERT: G 243 GLN cc_start: 0.7804 (mp10) cc_final: 0.7034 (mp10) REVERT: G 312 ASN cc_start: 0.9233 (m-40) cc_final: 0.8905 (m-40) REVERT: G 395 GLU cc_start: 0.8187 (mp0) cc_final: 0.7874 (mp0) REVERT: G 449 ASP cc_start: 0.7876 (t70) cc_final: 0.7472 (t70) REVERT: G 470 ASP cc_start: 0.8962 (m-30) cc_final: 0.8707 (m-30) REVERT: H 225 THR cc_start: 0.8032 (m) cc_final: 0.7585 (p) REVERT: H 231 ARG cc_start: 0.8759 (ptp90) cc_final: 0.8488 (mtm180) REVERT: H 243 GLN cc_start: 0.7928 (mp-120) cc_final: 0.7162 (mp-120) REVERT: H 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8957 (m-40) REVERT: H 395 GLU cc_start: 0.8123 (mp0) cc_final: 0.7867 (mp0) REVERT: H 449 ASP cc_start: 0.7841 (t70) cc_final: 0.7359 (t70) outliers start: 131 outliers final: 110 residues processed: 708 average time/residue: 0.1845 time to fit residues: 207.3851 Evaluate side-chains 722 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 600 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE 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 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 143 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 363 optimal weight: 0.4980 chunk 300 optimal weight: 0.0370 chunk 134 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN D 202 GLN D 441 GLN E 441 GLN F 93 HIS F 441 GLN G 93 HIS G 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.157013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.110070 restraints weight = 33330.889| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.95 r_work: 0.2901 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30593 Z= 0.117 Angle : 0.506 6.613 41496 Z= 0.266 Chirality : 0.042 0.153 4800 Planarity : 0.003 0.033 5160 Dihedral : 12.662 96.129 5247 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.75 % Allowed : 20.38 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3792 helix: 1.12 (0.14), residues: 1480 sheet: -0.49 (0.24), residues: 368 loop : -1.25 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 412 TYR 0.011 0.001 TYR H 353 PHE 0.016 0.001 PHE G 401 HIS 0.007 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00262 (30592) covalent geometry : angle 0.50564 (41496) hydrogen bonds : bond 0.02871 ( 1090) hydrogen bonds : angle 4.63155 ( 3078) Misc. bond : bond 0.00073 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 614 time to evaluate : 1.124 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7784 (tptt) cc_final: 0.7552 (tppt) REVERT: A 206 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7546 (mttm) REVERT: A 225 THR cc_start: 0.8174 (m) cc_final: 0.7688 (p) REVERT: A 243 GLN cc_start: 0.8052 (mp10) cc_final: 0.7268 (mp10) REVERT: A 277 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: A 286 MET cc_start: 0.8890 (tpp) cc_final: 0.8616 (tpp) REVERT: A 312 ASN cc_start: 0.9188 (m-40) cc_final: 0.8900 (m-40) REVERT: A 337 MET cc_start: 0.8900 (mmm) cc_final: 0.8442 (mtt) REVERT: A 420 MET cc_start: 0.6860 (mtt) cc_final: 0.6440 (mtt) REVERT: A 441 GLN cc_start: 0.8146 (mt0) cc_final: 0.7806 (mt0) REVERT: A 449 ASP cc_start: 0.7846 (t70) cc_final: 0.7374 (t70) REVERT: B 206 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7445 (mttm) REVERT: B 243 GLN cc_start: 0.7877 (mp-120) cc_final: 0.7564 (mp-120) REVERT: B 277 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: B 312 ASN cc_start: 0.9193 (m-40) cc_final: 0.8916 (m-40) REVERT: B 337 MET cc_start: 0.8770 (mmm) cc_final: 0.8389 (mtt) REVERT: B 395 GLU cc_start: 0.8145 (mp0) cc_final: 0.7850 (mp0) REVERT: B 441 GLN cc_start: 0.8245 (mt0) cc_final: 0.7583 (mt0) REVERT: C 135 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7859 (mpp) REVERT: C 225 THR cc_start: 0.7984 (m) cc_final: 0.7580 (p) REVERT: C 243 GLN cc_start: 0.7734 (mp10) cc_final: 0.7018 (mp10) REVERT: C 286 MET cc_start: 0.8902 (tpp) cc_final: 0.8604 (tpp) REVERT: C 312 ASN cc_start: 0.9185 (m-40) cc_final: 0.8904 (m-40) REVERT: C 449 ASP cc_start: 0.7623 (t0) cc_final: 0.7381 (t70) REVERT: D 103 GLU cc_start: 0.8648 (tp30) cc_final: 0.8432 (mm-30) REVERT: D 114 PHE cc_start: 0.8209 (m-10) cc_final: 0.7989 (m-10) REVERT: D 184 GLU cc_start: 0.2309 (OUTLIER) cc_final: 0.1463 (tp30) REVERT: D 243 GLN cc_start: 0.7778 (mp-120) cc_final: 0.7180 (mp-120) REVERT: D 286 MET cc_start: 0.8944 (tpp) cc_final: 0.8675 (tpp) REVERT: D 312 ASN cc_start: 0.9188 (m-40) cc_final: 0.8887 (m-40) REVERT: D 395 GLU cc_start: 0.8151 (mp0) cc_final: 0.7865 (mp0) REVERT: D 412 ARG cc_start: 0.7828 (ptt180) cc_final: 0.7627 (ptt180) REVERT: D 441 GLN cc_start: 0.8202 (mt0) cc_final: 0.7822 (mt0) REVERT: D 449 ASP cc_start: 0.7919 (t70) cc_final: 0.7517 (t70) REVERT: E 134 LYS cc_start: 0.7784 (tppt) cc_final: 0.7486 (tppt) REVERT: E 206 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7486 (mttm) REVERT: E 225 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7790 (p) REVERT: E 286 MET cc_start: 0.8915 (tpp) cc_final: 0.8652 (tpp) REVERT: E 312 ASN cc_start: 0.9212 (m-40) cc_final: 0.8941 (m-40) REVERT: E 395 GLU cc_start: 0.8145 (mp0) cc_final: 0.7902 (mp0) REVERT: E 441 GLN cc_start: 0.8168 (mt0) cc_final: 0.7813 (mt0) REVERT: E 448 GLN cc_start: 0.7694 (tt0) cc_final: 0.7453 (tt0) REVERT: F 202 GLN cc_start: 0.8282 (tt0) cc_final: 0.8080 (mm-40) REVERT: F 206 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7507 (mttm) REVERT: F 231 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7926 (mtm180) REVERT: F 312 ASN cc_start: 0.9192 (m-40) cc_final: 0.8922 (m-40) REVERT: F 337 MET cc_start: 0.8795 (mmm) cc_final: 0.8420 (mtt) REVERT: F 395 GLU cc_start: 0.8159 (mp0) cc_final: 0.7890 (mp0) REVERT: F 441 GLN cc_start: 0.8246 (mt0) cc_final: 0.7539 (mt0) REVERT: F 449 ASP cc_start: 0.7594 (t0) cc_final: 0.7385 (t70) REVERT: G 179 MET cc_start: 0.3957 (mtt) cc_final: 0.3170 (mpp) REVERT: G 206 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7247 (mttm) REVERT: G 243 GLN cc_start: 0.7805 (mp10) cc_final: 0.7032 (mp10) REVERT: G 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: G 312 ASN cc_start: 0.9183 (m-40) cc_final: 0.8869 (m-40) REVERT: G 395 GLU cc_start: 0.8201 (mp0) cc_final: 0.7896 (mp0) REVERT: G 441 GLN cc_start: 0.8177 (mt0) cc_final: 0.7803 (mt0) REVERT: G 449 ASP cc_start: 0.7843 (t70) cc_final: 0.7426 (t70) REVERT: H 47 ASP cc_start: 0.8688 (m-30) cc_final: 0.8247 (m-30) REVERT: H 225 THR cc_start: 0.7988 (m) cc_final: 0.7557 (p) REVERT: H 231 ARG cc_start: 0.8769 (ptp90) cc_final: 0.8498 (mtm180) REVERT: H 243 GLN cc_start: 0.7845 (mp-120) cc_final: 0.7089 (mp-120) REVERT: H 286 MET cc_start: 0.8925 (tpp) cc_final: 0.8700 (tpp) REVERT: H 312 ASN cc_start: 0.9186 (m-40) cc_final: 0.8904 (m-40) REVERT: H 337 MET cc_start: 0.8793 (mmm) cc_final: 0.8378 (mtt) REVERT: H 395 GLU cc_start: 0.8130 (mp0) cc_final: 0.7881 (mp0) REVERT: H 449 ASP cc_start: 0.7849 (t70) cc_final: 0.7383 (t70) outliers start: 117 outliers final: 98 residues processed: 699 average time/residue: 0.1793 time to fit residues: 199.6700 Evaluate side-chains 709 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 600 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE 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 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 HIS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE 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 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 121 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN F 93 HIS G 93 HIS G 202 GLN ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106630 restraints weight = 33848.547| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.97 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 30593 Z= 0.202 Angle : 0.555 6.658 41496 Z= 0.292 Chirality : 0.043 0.149 4800 Planarity : 0.004 0.036 5160 Dihedral : 12.784 89.325 5247 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.91 % Allowed : 20.29 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3792 helix: 1.00 (0.14), residues: 1480 sheet: -0.59 (0.24), residues: 352 loop : -1.27 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 412 TYR 0.014 0.002 TYR G 400 PHE 0.015 0.001 PHE C 401 HIS 0.014 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00463 (30592) covalent geometry : angle 0.55487 (41496) hydrogen bonds : bond 0.03404 ( 1090) hydrogen bonds : angle 4.81085 ( 3078) Misc. bond : bond 0.00126 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8422.95 seconds wall clock time: 144 minutes 38.96 seconds (8678.96 seconds total)