Starting phenix.real_space_refine on Thu Nov 20 08:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8r_20690/11_2025/6u8r_20690.cif" } resolution = 3.91 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= 0.084 sd= 3.293 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 176 5.16 5 C 19656 2.51 5 N 5400 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31528 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} 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: {'rna2p': 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: 7.85, per 1000 atoms: 0.25 Number of scatterers: 31528 At special positions: 0 Unit cell: (139.65, 148.05, 139.65, 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 176 16.00 P 72 15.00 O 6224 8.00 N 5400 7.00 C 19656 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 47 sheets defined 37.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.807A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (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 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.697A pdb=" N ARG A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.916A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.695A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.037A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.530A pdb=" N TYR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.608A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 486 removed outlier: 3.719A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 27 removed outlier: 5.095A pdb=" N PHE B 24 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN B 25 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 27 " --> pdb=" O PHE B 24 " (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: 3.542A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.672A pdb=" N GLN B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.107A pdb=" N LYS B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.887A pdb=" N GLU B 177 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.588A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.699A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.893A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.026A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.722A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) 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: 3.991A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.616A pdb=" N MET B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 472 removed outlier: 3.619A pdb=" N TYR B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.827A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' 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: 3.615A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.536A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.634A pdb=" N GLN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.736A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.513A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.636A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.588A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.602A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 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 75 through 85 Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.708A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.746A pdb=" N ASP D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.703A pdb=" N GLU D 177 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.612A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 removed outlier: 3.795A pdb=" N ASN D 230 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 4.000A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.802A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.161A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.729A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 removed outlier: 3.581A pdb=" N GLY D 472 " --> pdb=" O CYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.557A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (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 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.659A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.588A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.926A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.545A pdb=" N TYR E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 removed outlier: 3.656A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.618A pdb=" N VAL E 499 " --> pdb=" O SER E 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 27 removed outlier: 4.815A pdb=" N PHE F 24 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN F 25 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 27 " --> pdb=" O PHE F 24 " (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 75 through 86 removed outlier: 3.583A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.688A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.934A pdb=" N LYS F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.759A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU F 199 " --> pdb=" O LYS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.529A pdb=" N LYS F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.765A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.868A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 4.108A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.059A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) 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: 3.908A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 3.608A pdb=" N MET F 420 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 472 removed outlier: 3.602A pdb=" N TYR F 459 " --> pdb=" O LYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 495 through 502 removed outlier: 4.066A pdb=" N VAL F 499 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY F 501 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 495 through 502' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' 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 GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.752A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.737A pdb=" N GLN G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.058A pdb=" N ILE G 163 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.549A pdb=" N GLU G 177 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.618A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 258 through 265 removed outlier: 3.852A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.818A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 343 through 355 removed outlier: 3.878A pdb=" N LYS G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.988A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.813A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.549A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 removed outlier: 3.718A pdb=" N ASP H 162 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 159 through 163' Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.561A pdb=" N GLU H 177 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.561A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 removed outlier: 3.918A pdb=" N LYS H 228 " --> pdb=" O THR H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 4.040A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 263 " --> pdb=" O ARG H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.845A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.154A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.822A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 456 through 472 removed outlier: 3.647A pdb=" N GLY H 472 " --> pdb=" O CYS H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 497 through 502 Processing helix chain 'M' and resid 3 through 8 removed outlier: 4.460A pdb=" N SER M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.512A pdb=" N LEU I 5 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE I 6 " --> pdb=" O ASP I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 6' Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'K' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.618A pdb=" N LYS A 489 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.795A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 271 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.739A pdb=" N LEU A 408 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 403 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.852A pdb=" N SER A 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 403 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.134A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.735A pdb=" N ILE B 142 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 157 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 144 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AB3, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.853A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.839A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 248 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.877A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.664A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.763A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP D 274 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 7.664A pdb=" N ILE D 142 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE D 157 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE D 144 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.221A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 209 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 38 removed outlier: 4.654A pdb=" N LYS E 489 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.798A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AD1, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.665A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.615A pdb=" N LEU E 408 " --> pdb=" O PHE E 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 403 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.830A pdb=" N SER E 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER H 403 " --> pdb=" O ILE H 406 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 67 removed outlier: 7.330A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 145 removed outlier: 6.562A pdb=" N ILE F 142 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE F 157 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE F 144 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 211 through 212 Processing sheet with id=AD9, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.783A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.974A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 143 through 144 Processing sheet with id=AE5, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.011A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.642A pdb=" N LYS G 409 " --> pdb=" O VAL G 447 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER H 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.938A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 143 through 145 removed outlier: 3.891A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 208 through 213 removed outlier: 6.875A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2700 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: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5311 1.30 - 1.43: 7761 1.43 - 1.56: 18536 1.56 - 1.69: 160 1.69 - 1.82: 304 Bond restraints: 32072 Sorted by residual: bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.244 0.287 1.20e-02 6.94e+03 5.71e+02 bond pdb=" C2' ATP H 602 " pdb=" C3' ATP H 602 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.70e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.68e+02 bond pdb=" C2' ATP A 604 " pdb=" C3' ATP A 604 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.68e+02 bond pdb=" C2' ATP E 604 " pdb=" C3' ATP E 604 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.64e+02 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.62: 42393 4.62 - 9.23: 887 9.23 - 13.85: 101 13.85 - 18.47: 72 18.47 - 23.08: 35 Bond angle restraints: 43488 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 116.79 23.08 1.00e+00 1.00e+00 5.33e+02 angle pdb=" PB ATP H 602 " pdb=" O3B ATP H 602 " pdb=" PG ATP H 602 " ideal model delta sigma weight residual 139.87 117.45 22.42 1.00e+00 1.00e+00 5.02e+02 angle pdb=" PB ATP G 602 " pdb=" O3B ATP G 602 " pdb=" PG ATP G 602 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 ... (remaining 43483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.57: 17886 20.57 - 41.15: 1471 41.15 - 61.72: 370 61.72 - 82.30: 112 82.30 - 102.87: 17 Dihedral angle restraints: 19856 sinusoidal: 8448 harmonic: 11408 Sorted by residual: dihedral pdb=" CA ASP D 164 " pdb=" C ASP D 164 " pdb=" N PHE D 165 " pdb=" CA PHE D 165 " ideal model delta harmonic sigma weight residual -180.00 -143.66 -36.34 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 143.81 36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA LYS D 62 " pdb=" C LYS D 62 " pdb=" N THR D 63 " pdb=" CA THR D 63 " ideal model delta harmonic sigma weight residual 180.00 148.44 31.56 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4350 0.122 - 0.244: 562 0.244 - 0.366: 50 0.366 - 0.488: 4 0.488 - 0.610: 2 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 362 " pdb=" CA ILE G 362 " pdb=" CG1 ILE G 362 " pdb=" CG2 ILE G 362 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB ILE H 300 " pdb=" CA ILE H 300 " pdb=" CG1 ILE H 300 " pdb=" CG2 ILE H 300 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 4965 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 411 " -0.021 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR C 411 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 411 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 411 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 411 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 411 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 411 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 411 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO H 64 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 111 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C GLU F 111 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU F 111 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN F 112 " -0.017 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4602 2.73 - 3.27: 30827 3.27 - 3.82: 55756 3.82 - 4.36: 63232 4.36 - 4.90: 104238 Nonbonded interactions: 258655 Sorted by model distance: nonbonded pdb=" OG SER A 329 " pdb=" O HIS B 504 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR H 147 " pdb=" OG SER H 152 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP G 50 " pdb=" OG SER G 475 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP D 364 " pdb=" O2' IMP D 603 " model vdw 2.238 3.040 nonbonded pdb=" OG SER E 159 " pdb=" O1B ATP E 603 " model vdw 2.242 3.040 ... (remaining 258650 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' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.060 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.019 0.287 32073 Z= 1.098 Angle : 1.844 23.084 43488 Z= 1.144 Chirality : 0.085 0.610 4968 Planarity : 0.008 0.081 5448 Dihedral : 17.004 102.870 12576 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.74 % Favored : 90.98 % Rotamer: Outliers : 3.21 % Allowed : 12.32 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.40 (0.11), residues: 3968 helix: -3.72 (0.09), residues: 1247 sheet: -2.56 (0.22), residues: 432 loop : -2.57 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B 355 TYR 0.058 0.004 TYR C 411 PHE 0.044 0.005 PHE F 174 HIS 0.017 0.003 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.01881 (32072) covalent geometry : angle 1.84428 (43488) hydrogen bonds : bond 0.22090 ( 961) hydrogen bonds : angle 8.67212 ( 2700) Misc. bond : bond 0.00309 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1179 time to evaluate : 0.961 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8392 (t70) cc_final: 0.8191 (t70) REVERT: A 173 CYS cc_start: 0.5872 (m) cc_final: 0.5473 (m) REVERT: A 195 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8115 (tptt) REVERT: A 224 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8262 (tpp80) REVERT: A 230 ASN cc_start: 0.9417 (t160) cc_final: 0.9168 (t0) REVERT: A 246 CYS cc_start: 0.9023 (t) cc_final: 0.8500 (t) REVERT: A 273 LEU cc_start: 0.9689 (mt) cc_final: 0.9442 (mt) REVERT: A 274 ASP cc_start: 0.9017 (t0) cc_final: 0.8701 (t0) REVERT: A 352 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 357 PHE cc_start: 0.9219 (m-80) cc_final: 0.8859 (m-10) REVERT: A 483 MET cc_start: 0.9441 (tmm) cc_final: 0.8811 (tmm) REVERT: B 16 ASP cc_start: 0.9024 (t0) cc_final: 0.8769 (t0) REVERT: B 41 TYR cc_start: 0.8887 (t80) cc_final: 0.8668 (t80) REVERT: B 51 LEU cc_start: 0.8851 (tp) cc_final: 0.8500 (tt) REVERT: B 103 GLU cc_start: 0.8857 (mp0) cc_final: 0.8549 (mp0) REVERT: B 105 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8430 (ptp-110) REVERT: B 158 ILE cc_start: 0.8988 (mm) cc_final: 0.8757 (mm) REVERT: B 179 MET cc_start: 0.7408 (pp-130) cc_final: 0.7064 (pp-130) REVERT: B 274 ASP cc_start: 0.8963 (t0) cc_final: 0.8601 (t0) REVERT: B 277 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9007 (tm-30) REVERT: B 309 GLN cc_start: 0.9266 (pm20) cc_final: 0.8828 (pm20) REVERT: B 335 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 409 LYS cc_start: 0.8473 (mttp) cc_final: 0.7529 (mmtt) REVERT: B 467 SER cc_start: 0.9464 (p) cc_final: 0.9245 (p) REVERT: B 487 GLU cc_start: 0.9078 (tt0) cc_final: 0.8680 (tt0) REVERT: C 21 GLN cc_start: 0.8822 (pp30) cc_final: 0.8362 (pp30) REVERT: C 25 ASN cc_start: 0.8712 (t0) cc_final: 0.8137 (t0) REVERT: C 28 ASP cc_start: 0.8730 (m-30) cc_final: 0.8518 (m-30) REVERT: C 48 GLN cc_start: 0.9030 (mt0) cc_final: 0.8399 (mt0) REVERT: C 94 ASN cc_start: 0.9230 (t0) cc_final: 0.8648 (t0) REVERT: C 105 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8186 (ttp80) REVERT: C 110 TYR cc_start: 0.8768 (t80) cc_final: 0.8322 (t80) REVERT: C 182 ARG cc_start: 0.8316 (tpm170) cc_final: 0.7939 (tpp-160) REVERT: C 200 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8668 (mt) REVERT: C 206 LYS cc_start: 0.9185 (tppp) cc_final: 0.8688 (tppp) REVERT: C 210 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.9085 (Cg_endo) REVERT: C 216 ASP cc_start: 0.7862 (t0) cc_final: 0.7597 (t0) REVERT: C 224 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8511 (ttm-80) REVERT: C 238 LYS cc_start: 0.8916 (mppt) cc_final: 0.8588 (mmmm) REVERT: C 262 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9143 (tt) REVERT: C 277 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 296 ASN cc_start: 0.8716 (p0) cc_final: 0.8400 (m-40) REVERT: C 343 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 386 MET cc_start: 0.8500 (mpm) cc_final: 0.8125 (mpm) REVERT: C 461 ILE cc_start: 0.9219 (pp) cc_final: 0.8814 (pp) REVERT: C 465 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: C 468 CYS cc_start: 0.8477 (t) cc_final: 0.8175 (t) REVERT: C 475 SER cc_start: 0.8755 (t) cc_final: 0.8410 (t) REVERT: C 483 MET cc_start: 0.9093 (tmm) cc_final: 0.8870 (tmm) REVERT: D 32 TYR cc_start: 0.9169 (m-10) cc_final: 0.8711 (m-10) REVERT: D 93 HIS cc_start: 0.8825 (p-80) cc_final: 0.8593 (p90) REVERT: D 112 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 327 SER cc_start: 0.8979 (p) cc_final: 0.8720 (p) REVERT: D 334 GLN cc_start: 0.8967 (mt0) cc_final: 0.8520 (mt0) REVERT: D 335 GLU cc_start: 0.7910 (tt0) cc_final: 0.7679 (tt0) REVERT: D 343 GLN cc_start: 0.8799 (tm130) cc_final: 0.8436 (tm-30) REVERT: D 400 TYR cc_start: 0.7644 (m-80) cc_final: 0.7442 (m-80) REVERT: D 450 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8563 (mmmt) REVERT: D 482 MET cc_start: 0.9090 (mtp) cc_final: 0.8843 (mtp) REVERT: D 483 MET cc_start: 0.9744 (tmm) cc_final: 0.9527 (tmm) REVERT: D 510 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8169 (tm-30) REVERT: E 75 GLU cc_start: 0.8301 (mp0) cc_final: 0.7694 (mp0) REVERT: E 150 MET cc_start: 0.7322 (tmt) cc_final: 0.6779 (tmt) REVERT: E 174 PHE cc_start: 0.8976 (m-80) cc_final: 0.8457 (m-80) REVERT: E 241 LYS cc_start: 0.9224 (mptt) cc_final: 0.8932 (mmtm) REVERT: E 273 LEU cc_start: 0.9629 (mp) cc_final: 0.9425 (mp) REVERT: E 274 ASP cc_start: 0.9308 (t0) cc_final: 0.9037 (t0) REVERT: E 279 ASN cc_start: 0.8555 (t0) cc_final: 0.8285 (t0) REVERT: E 285 ASN cc_start: 0.8976 (m110) cc_final: 0.8536 (m110) REVERT: E 296 ASN cc_start: 0.8503 (p0) cc_final: 0.8117 (t0) REVERT: E 382 SER cc_start: 0.9635 (m) cc_final: 0.9391 (t) REVERT: E 385 MET cc_start: 0.8972 (ttp) cc_final: 0.8741 (ttm) REVERT: E 455 LYS cc_start: 0.8969 (tppt) cc_final: 0.8489 (mmmt) REVERT: E 500 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 16 ASP cc_start: 0.8842 (t0) cc_final: 0.8475 (t0) REVERT: F 51 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8669 (tm) REVERT: F 103 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: F 105 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8444 (mtm110) REVERT: F 110 TYR cc_start: 0.8662 (t80) cc_final: 0.8230 (t80) REVERT: F 114 PHE cc_start: 0.9189 (m-10) cc_final: 0.8753 (m-80) REVERT: F 132 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: F 206 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8888 (mtpt) REVERT: F 283 GLN cc_start: 0.9050 (tt0) cc_final: 0.8739 (tt0) REVERT: F 319 ASP cc_start: 0.8022 (t0) cc_final: 0.7569 (t0) REVERT: F 335 GLU cc_start: 0.8452 (tt0) cc_final: 0.8191 (tt0) REVERT: F 409 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8538 (tttt) REVERT: F 483 MET cc_start: 0.9408 (tmm) cc_final: 0.8999 (tmm) REVERT: F 487 GLU cc_start: 0.9120 (tt0) cc_final: 0.8771 (tt0) REVERT: G 75 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8055 (mt-10) REVERT: G 95 CYS cc_start: 0.8379 (p) cc_final: 0.8028 (p) REVERT: G 98 GLU cc_start: 0.8605 (pm20) cc_final: 0.8219 (pm20) REVERT: G 100 GLN cc_start: 0.8580 (pm20) cc_final: 0.8248 (pm20) REVERT: G 105 ARG cc_start: 0.8885 (mtm110) cc_final: 0.8426 (ttp80) REVERT: G 200 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8559 (mp) REVERT: G 277 GLN cc_start: 0.8673 (tm130) cc_final: 0.8094 (tm130) REVERT: G 296 ASN cc_start: 0.8773 (p0) cc_final: 0.8470 (m-40) REVERT: G 343 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 355 ARG cc_start: 0.9402 (ptt180) cc_final: 0.9195 (ptt90) REVERT: G 362 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9144 (tp) REVERT: G 369 ASN cc_start: 0.8975 (p0) cc_final: 0.8771 (p0) REVERT: G 383 THR cc_start: 0.9762 (p) cc_final: 0.9508 (p) REVERT: G 386 MET cc_start: 0.8537 (mmp) cc_final: 0.8233 (mmm) REVERT: G 461 ILE cc_start: 0.9162 (pp) cc_final: 0.8722 (pp) REVERT: G 465 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: G 499 VAL cc_start: 0.9273 (p) cc_final: 0.9000 (p) REVERT: H 32 TYR cc_start: 0.9050 (m-10) cc_final: 0.8594 (m-10) REVERT: H 93 HIS cc_start: 0.8869 (p-80) cc_final: 0.8648 (p90) REVERT: H 103 GLU cc_start: 0.8541 (mp0) cc_final: 0.8306 (mp0) REVERT: H 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8408 (tmtt) REVERT: H 277 GLN cc_start: 0.8757 (tm130) cc_final: 0.8440 (tm130) REVERT: H 281 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7747 (pp) REVERT: H 327 SER cc_start: 0.8869 (p) cc_final: 0.8517 (p) REVERT: H 334 GLN cc_start: 0.9067 (mt0) cc_final: 0.8853 (mt0) REVERT: H 343 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8594 (tm-30) REVERT: H 364 ASP cc_start: 0.8495 (m-30) cc_final: 0.8147 (m-30) REVERT: H 385 MET cc_start: 0.8611 (ttm) cc_final: 0.8403 (ttm) REVERT: H 386 MET cc_start: 0.8526 (mtm) cc_final: 0.8308 (mtm) REVERT: H 393 THR cc_start: 0.8250 (p) cc_final: 0.7643 (p) REVERT: H 395 GLU cc_start: 0.8646 (mp0) cc_final: 0.8267 (mp0) outliers start: 105 outliers final: 22 residues processed: 1216 average time/residue: 0.1939 time to fit residues: 383.8806 Evaluate side-chains 929 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 897 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.0050 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 230 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 93 HIS B 137 HIS B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN D 22 GLN D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN E 230 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 HIS F 22 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 507 HIS G 22 GLN G 25 ASN G 48 GLN G 94 ASN G 277 GLN G 283 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN G 478 GLN H 253 HIS H 277 GLN H 285 ASN H 298 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN H 478 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.097419 restraints weight = 51961.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.101402 restraints weight = 26435.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104030 restraints weight = 16617.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105960 restraints weight = 11988.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107092 restraints weight = 9452.659| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32073 Z= 0.155 Angle : 0.835 14.537 43488 Z= 0.419 Chirality : 0.050 0.277 4968 Planarity : 0.005 0.049 5448 Dihedral : 15.234 88.866 5430 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % Rotamer: Outliers : 5.35 % Allowed : 20.23 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.32 (0.12), residues: 3968 helix: -2.31 (0.12), residues: 1272 sheet: -2.35 (0.22), residues: 424 loop : -2.13 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 105 TYR 0.026 0.002 TYR A 353 PHE 0.026 0.002 PHE D 131 HIS 0.008 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00347 (32072) covalent geometry : angle 0.83498 (43488) hydrogen bonds : bond 0.04390 ( 961) hydrogen bonds : angle 6.41862 ( 2700) Misc. bond : bond 0.00205 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1092 time to evaluate : 1.207 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 34 ASP cc_start: 0.8285 (t70) cc_final: 0.8053 (t70) REVERT: A 100 GLN cc_start: 0.9384 (tt0) cc_final: 0.9141 (tt0) REVERT: A 105 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8106 (ttm-80) REVERT: A 108 LYS cc_start: 0.9281 (mtpt) cc_final: 0.9047 (mmtt) REVERT: A 110 TYR cc_start: 0.8018 (t80) cc_final: 0.7613 (t80) REVERT: A 112 GLN cc_start: 0.7811 (mp10) cc_final: 0.6824 (mp10) REVERT: A 145 THR cc_start: 0.8894 (p) cc_final: 0.8597 (t) REVERT: A 173 CYS cc_start: 0.5226 (m) cc_final: 0.4931 (m) REVERT: A 238 LYS cc_start: 0.8435 (mtmp) cc_final: 0.8154 (mtmm) REVERT: A 274 ASP cc_start: 0.8818 (t0) cc_final: 0.8489 (t0) REVERT: A 335 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8702 (tm-30) REVERT: A 404 ASP cc_start: 0.8549 (t70) cc_final: 0.8251 (t0) REVERT: A 409 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8637 (ttmm) REVERT: A 496 SER cc_start: 0.9228 (m) cc_final: 0.9011 (p) REVERT: A 500 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 64 PRO cc_start: 0.9480 (Cg_endo) cc_final: 0.9256 (Cg_exo) REVERT: B 103 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: B 105 ARG cc_start: 0.8718 (mtm110) cc_final: 0.8408 (ptp-110) REVERT: B 158 ILE cc_start: 0.8989 (mm) cc_final: 0.8783 (mm) REVERT: B 160 SER cc_start: 0.8633 (t) cc_final: 0.7939 (m) REVERT: B 179 MET cc_start: 0.7379 (pp-130) cc_final: 0.7012 (pp-130) REVERT: B 231 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8690 (mmp80) REVERT: B 274 ASP cc_start: 0.9054 (t0) cc_final: 0.8837 (t0) REVERT: B 312 ASN cc_start: 0.9378 (m-40) cc_final: 0.8557 (t0) REVERT: B 334 GLN cc_start: 0.8945 (mt0) cc_final: 0.8487 (mt0) REVERT: B 335 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 343 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8041 (tp-100) REVERT: B 355 ARG cc_start: 0.9098 (ttp-170) cc_final: 0.8838 (ttp80) REVERT: B 395 GLU cc_start: 0.8689 (mp0) cc_final: 0.8479 (mp0) REVERT: B 408 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8262 (pp) REVERT: B 409 LYS cc_start: 0.8171 (mttp) cc_final: 0.7742 (mmtt) REVERT: B 487 GLU cc_start: 0.9122 (tt0) cc_final: 0.8627 (tt0) REVERT: B 498 GLN cc_start: 0.8286 (mm110) cc_final: 0.8012 (mm110) REVERT: B 510 GLU cc_start: 0.8295 (tt0) cc_final: 0.8051 (tt0) REVERT: C 25 ASN cc_start: 0.8641 (t0) cc_final: 0.8186 (t0) REVERT: C 36 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 105 ARG cc_start: 0.8697 (mtm110) cc_final: 0.8281 (ttp80) REVERT: C 110 TYR cc_start: 0.8627 (t80) cc_final: 0.8229 (t80) REVERT: C 134 LYS cc_start: 0.9318 (ptmm) cc_final: 0.9050 (tptt) REVERT: C 182 ARG cc_start: 0.8126 (tpm170) cc_final: 0.7648 (tpp-160) REVERT: C 206 LYS cc_start: 0.9122 (tppp) cc_final: 0.8802 (mmmm) REVERT: C 210 PRO cc_start: 0.9255 (Cg_exo) cc_final: 0.9054 (Cg_endo) REVERT: C 224 ARG cc_start: 0.8952 (ttt-90) cc_final: 0.8347 (ttm-80) REVERT: C 277 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 279 ASN cc_start: 0.8994 (t0) cc_final: 0.8602 (t0) REVERT: C 297 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9115 (tm) REVERT: C 355 ARG cc_start: 0.9248 (ptt90) cc_final: 0.9032 (ptm-80) REVERT: C 369 ASN cc_start: 0.8680 (p0) cc_final: 0.8194 (p0) REVERT: C 386 MET cc_start: 0.8420 (mpm) cc_final: 0.7975 (mpm) REVERT: C 409 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7884 (ptpt) REVERT: C 468 CYS cc_start: 0.8678 (t) cc_final: 0.8351 (t) REVERT: C 480 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8821 (mtt90) REVERT: C 483 MET cc_start: 0.9207 (tmm) cc_final: 0.8675 (tmm) REVERT: D 32 TYR cc_start: 0.8931 (m-10) cc_final: 0.8324 (m-10) REVERT: D 65 LEU cc_start: 0.9454 (mm) cc_final: 0.9232 (mm) REVERT: D 75 GLU cc_start: 0.7659 (pp20) cc_final: 0.7376 (pp20) REVERT: D 103 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: D 106 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8784 (ttpt) REVERT: D 199 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8851 (tm-30) REVERT: D 227 LEU cc_start: 0.9090 (mp) cc_final: 0.8823 (mm) REVERT: D 230 ASN cc_start: 0.7792 (t0) cc_final: 0.7089 (t0) REVERT: D 285 ASN cc_start: 0.9163 (m110) cc_final: 0.8951 (m110) REVERT: D 327 SER cc_start: 0.9093 (p) cc_final: 0.8755 (t) REVERT: D 482 MET cc_start: 0.9239 (mtp) cc_final: 0.8925 (mtp) REVERT: D 483 MET cc_start: 0.9825 (tmm) cc_final: 0.9426 (tmm) REVERT: D 510 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8117 (tm-30) REVERT: E 13 VAL cc_start: 0.9583 (t) cc_final: 0.9294 (p) REVERT: E 16 ASP cc_start: 0.8894 (t70) cc_final: 0.8665 (t0) REVERT: E 72 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9165 (t) REVERT: E 75 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: E 150 MET cc_start: 0.6962 (tmt) cc_final: 0.6264 (tmt) REVERT: E 179 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6427 (ppp) REVERT: E 224 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8409 (ttm-80) REVERT: E 230 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8875 (t0) REVERT: E 238 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8007 (mtmm) REVERT: E 241 LYS cc_start: 0.9236 (mptt) cc_final: 0.8895 (mmtm) REVERT: E 279 ASN cc_start: 0.8709 (t0) cc_final: 0.7732 (t0) REVERT: E 296 ASN cc_start: 0.8416 (p0) cc_final: 0.8069 (t0) REVERT: E 335 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8275 (tm-30) REVERT: E 395 GLU cc_start: 0.8629 (mp0) cc_final: 0.8414 (mp0) REVERT: E 466 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8011 (t-90) REVERT: E 480 ARG cc_start: 0.9289 (mtm-85) cc_final: 0.9082 (mtt90) REVERT: E 482 MET cc_start: 0.8754 (mtm) cc_final: 0.8553 (mtp) REVERT: E 483 MET cc_start: 0.9422 (tmm) cc_final: 0.8788 (tmm) REVERT: E 500 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8785 (tm-30) REVERT: F 16 ASP cc_start: 0.8821 (t0) cc_final: 0.8394 (t0) REVERT: F 51 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (tm) REVERT: F 105 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8425 (ptp-110) REVERT: F 110 TYR cc_start: 0.8689 (t80) cc_final: 0.8291 (t80) REVERT: F 114 PHE cc_start: 0.9081 (m-10) cc_final: 0.8646 (m-80) REVERT: F 121 LEU cc_start: 0.8278 (tt) cc_final: 0.8055 (tt) REVERT: F 203 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8780 (mtm110) REVERT: F 206 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8689 (mmmm) REVERT: F 279 ASN cc_start: 0.8677 (t0) cc_final: 0.8314 (t0) REVERT: F 319 ASP cc_start: 0.8017 (t0) cc_final: 0.7762 (m-30) REVERT: F 409 LYS cc_start: 0.8556 (ttmm) cc_final: 0.7485 (tttt) REVERT: F 412 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7209 (ptt90) REVERT: F 482 MET cc_start: 0.8771 (mtp) cc_final: 0.8359 (mtp) REVERT: G 75 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8143 (mm-30) REVERT: G 94 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8636 (t0) REVERT: G 105 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8350 (ttp80) REVERT: G 195 LYS cc_start: 0.9236 (pmmt) cc_final: 0.8495 (tttt) REVERT: G 277 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 355 ARG cc_start: 0.9269 (ptt180) cc_final: 0.9060 (ptt180) REVERT: G 386 MET cc_start: 0.8733 (mmp) cc_final: 0.8482 (mmm) REVERT: G 390 LEU cc_start: 0.9009 (mp) cc_final: 0.8535 (mp) REVERT: G 478 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7374 (pp30) REVERT: G 510 GLU cc_start: 0.8283 (mp0) cc_final: 0.8056 (mp0) REVERT: H 32 TYR cc_start: 0.8734 (m-10) cc_final: 0.8255 (m-10) REVERT: H 33 ASN cc_start: 0.8349 (t0) cc_final: 0.7602 (t0) REVERT: H 75 GLU cc_start: 0.8418 (mp0) cc_final: 0.8187 (mp0) REVERT: H 82 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8900 (mtm) REVERT: H 93 HIS cc_start: 0.8894 (p-80) cc_final: 0.8576 (p90) REVERT: H 131 PHE cc_start: 0.9167 (m-80) cc_final: 0.8529 (m-80) REVERT: H 228 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8115 (tmtt) REVERT: H 231 ARG cc_start: 0.8517 (mmp80) cc_final: 0.8250 (mmp-170) REVERT: H 274 ASP cc_start: 0.9022 (t70) cc_final: 0.8667 (t70) REVERT: H 286 MET cc_start: 0.8474 (mtp) cc_final: 0.8200 (mtp) REVERT: H 327 SER cc_start: 0.8625 (p) cc_final: 0.8374 (p) REVERT: H 343 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7629 (tm-30) REVERT: H 393 THR cc_start: 0.8127 (p) cc_final: 0.7482 (p) REVERT: H 395 GLU cc_start: 0.8577 (mp0) cc_final: 0.8104 (mp0) REVERT: H 465 GLN cc_start: 0.8912 (mt0) cc_final: 0.8623 (mt0) REVERT: H 510 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8103 (tm-30) outliers start: 175 outliers final: 88 residues processed: 1170 average time/residue: 0.1932 time to fit residues: 368.7673 Evaluate side-chains 1014 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 911 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain J residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 281 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 391 optimal weight: 0.0030 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 369 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 387 optimal weight: 8.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 137 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 137 HIS H 243 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098642 restraints weight = 52153.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102660 restraints weight = 26840.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105424 restraints weight = 16942.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107202 restraints weight = 12194.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108535 restraints weight = 9725.670| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32073 Z= 0.140 Angle : 0.780 14.684 43488 Z= 0.388 Chirality : 0.049 0.353 4968 Planarity : 0.004 0.042 5448 Dihedral : 14.091 88.758 5393 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.46 % Favored : 92.44 % Rotamer: Outliers : 5.90 % Allowed : 23.20 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.92 (0.12), residues: 3968 helix: -1.77 (0.13), residues: 1274 sheet: -2.21 (0.24), residues: 374 loop : -2.02 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 105 TYR 0.028 0.002 TYR F 484 PHE 0.019 0.001 PHE D 165 HIS 0.014 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00316 (32072) covalent geometry : angle 0.78012 (43488) hydrogen bonds : bond 0.04019 ( 961) hydrogen bonds : angle 6.01031 ( 2700) Misc. bond : bond 0.00181 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1037 time to evaluate : 1.092 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 82 MET cc_start: 0.9401 (mmm) cc_final: 0.9140 (tpp) REVERT: A 100 GLN cc_start: 0.9342 (tt0) cc_final: 0.9038 (tt0) REVERT: A 105 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8053 (ttm-80) REVERT: A 125 ASP cc_start: 0.7728 (p0) cc_final: 0.7489 (p0) REVERT: A 229 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8512 (mtpp) REVERT: A 230 ASN cc_start: 0.9140 (t0) cc_final: 0.8924 (t0) REVERT: A 238 LYS cc_start: 0.8407 (mtmp) cc_final: 0.8101 (mtmm) REVERT: A 274 ASP cc_start: 0.8859 (t0) cc_final: 0.8640 (t0) REVERT: A 279 ASN cc_start: 0.8660 (t0) cc_final: 0.7768 (t0) REVERT: A 352 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 404 ASP cc_start: 0.8563 (t70) cc_final: 0.8233 (t0) REVERT: A 409 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8610 (ttmm) REVERT: A 412 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6934 (ptt90) REVERT: A 478 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8650 (pt0) REVERT: A 489 LYS cc_start: 0.9322 (mttt) cc_final: 0.9108 (mmtp) REVERT: A 496 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8374 (p) REVERT: A 500 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8823 (tm-30) REVERT: B 160 SER cc_start: 0.8514 (t) cc_final: 0.7837 (m) REVERT: B 179 MET cc_start: 0.7286 (pp-130) cc_final: 0.6980 (pp-130) REVERT: B 231 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8701 (mmp80) REVERT: B 259 ARG cc_start: 0.8854 (mtp-110) cc_final: 0.8184 (ttm-80) REVERT: B 277 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 334 GLN cc_start: 0.9003 (mt0) cc_final: 0.8547 (mt0) REVERT: B 335 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 386 MET cc_start: 0.8690 (ptp) cc_final: 0.8416 (ptp) REVERT: B 408 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8165 (pp) REVERT: B 409 LYS cc_start: 0.8139 (mttp) cc_final: 0.7717 (mmtt) REVERT: B 487 GLU cc_start: 0.9148 (tt0) cc_final: 0.8623 (tt0) REVERT: B 498 GLN cc_start: 0.8352 (mm110) cc_final: 0.8144 (mm-40) REVERT: B 510 GLU cc_start: 0.8319 (tt0) cc_final: 0.8102 (tt0) REVERT: C 25 ASN cc_start: 0.8554 (t0) cc_final: 0.7968 (t0) REVERT: C 36 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8794 (pp) REVERT: C 105 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8230 (ttp80) REVERT: C 110 TYR cc_start: 0.8478 (t80) cc_final: 0.8263 (t80) REVERT: C 134 LYS cc_start: 0.9321 (ptmm) cc_final: 0.9048 (tptt) REVERT: C 150 MET cc_start: 0.8001 (tpp) cc_final: 0.7720 (tpp) REVERT: C 164 ASP cc_start: 0.6761 (m-30) cc_final: 0.6481 (m-30) REVERT: C 182 ARG cc_start: 0.8154 (tpm170) cc_final: 0.7623 (tpp-160) REVERT: C 206 LYS cc_start: 0.9132 (tppp) cc_final: 0.8768 (mmmm) REVERT: C 218 LEU cc_start: 0.9487 (pt) cc_final: 0.9033 (tt) REVERT: C 224 ARG cc_start: 0.8882 (ttt-90) cc_final: 0.8343 (ttm-80) REVERT: C 277 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 279 ASN cc_start: 0.8899 (t0) cc_final: 0.8523 (t0) REVERT: C 297 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9099 (tm) REVERT: C 386 MET cc_start: 0.8393 (mpm) cc_final: 0.7966 (mpm) REVERT: C 467 SER cc_start: 0.9704 (m) cc_final: 0.9447 (t) REVERT: C 468 CYS cc_start: 0.8765 (t) cc_final: 0.8311 (t) REVERT: C 478 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: C 483 MET cc_start: 0.9200 (tmm) cc_final: 0.8683 (tmm) REVERT: C 484 TYR cc_start: 0.9125 (m-80) cc_final: 0.8644 (m-10) REVERT: D 34 ASP cc_start: 0.7899 (t0) cc_final: 0.7678 (m-30) REVERT: D 103 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: D 199 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8903 (tm-30) REVERT: D 277 GLN cc_start: 0.9085 (tp40) cc_final: 0.8853 (tp40) REVERT: D 285 ASN cc_start: 0.9182 (m110) cc_final: 0.8906 (m110) REVERT: D 327 SER cc_start: 0.9044 (p) cc_final: 0.8716 (t) REVERT: D 343 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 359 VAL cc_start: 0.9321 (t) cc_final: 0.9097 (p) REVERT: D 482 MET cc_start: 0.9254 (mtp) cc_final: 0.8950 (mtp) REVERT: D 483 MET cc_start: 0.9826 (tmm) cc_final: 0.9459 (tmm) REVERT: E 16 ASP cc_start: 0.8900 (t70) cc_final: 0.8540 (t0) REVERT: E 72 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9198 (t) REVERT: E 75 GLU cc_start: 0.8154 (mp0) cc_final: 0.7814 (mp0) REVERT: E 105 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.7872 (ttm-80) REVERT: E 150 MET cc_start: 0.7052 (tmt) cc_final: 0.6395 (tmt) REVERT: E 224 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (ttm-80) REVERT: E 230 ASN cc_start: 0.8841 (t0) cc_final: 0.8549 (t0) REVERT: E 241 LYS cc_start: 0.9201 (mptt) cc_final: 0.8846 (mmtm) REVERT: E 279 ASN cc_start: 0.8669 (t0) cc_final: 0.7706 (t0) REVERT: E 285 ASN cc_start: 0.8841 (m110) cc_final: 0.8404 (m110) REVERT: E 296 ASN cc_start: 0.8294 (p0) cc_final: 0.8009 (t0) REVERT: E 466 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: E 483 MET cc_start: 0.9469 (tmm) cc_final: 0.9248 (tmm) REVERT: E 500 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8850 (tm-30) REVERT: F 16 ASP cc_start: 0.8758 (t0) cc_final: 0.8290 (t0) REVERT: F 51 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8066 (tm) REVERT: F 105 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8499 (ptp-110) REVERT: F 110 TYR cc_start: 0.8654 (t80) cc_final: 0.8346 (t80) REVERT: F 114 PHE cc_start: 0.9023 (m-10) cc_final: 0.8477 (m-80) REVERT: F 121 LEU cc_start: 0.8297 (tt) cc_final: 0.8085 (tt) REVERT: F 203 ARG cc_start: 0.9072 (mtm110) cc_final: 0.8837 (mtm110) REVERT: F 206 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8687 (mmmm) REVERT: F 259 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: F 319 ASP cc_start: 0.8028 (t0) cc_final: 0.7711 (m-30) REVERT: F 359 VAL cc_start: 0.9269 (t) cc_final: 0.8982 (p) REVERT: F 395 GLU cc_start: 0.8802 (mp0) cc_final: 0.8379 (mp0) REVERT: F 409 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8085 (mttt) REVERT: F 412 ARG cc_start: 0.8120 (ttp80) cc_final: 0.6889 (ptt90) REVERT: F 482 MET cc_start: 0.8684 (mtp) cc_final: 0.8197 (mtp) REVERT: F 483 MET cc_start: 0.9143 (tmm) cc_final: 0.8907 (tmm) REVERT: F 487 GLU cc_start: 0.9195 (tt0) cc_final: 0.8940 (tt0) REVERT: G 78 MET cc_start: 0.8473 (tpp) cc_final: 0.8264 (mpp) REVERT: G 105 ARG cc_start: 0.8748 (mtm110) cc_final: 0.8370 (ttp80) REVERT: G 153 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7720 (tpp80) REVERT: G 195 LYS cc_start: 0.9260 (pmmt) cc_final: 0.8566 (tttt) REVERT: G 238 LYS cc_start: 0.9291 (mtmm) cc_final: 0.8780 (mtpp) REVERT: G 277 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7719 (tm-30) REVERT: G 355 ARG cc_start: 0.9291 (ptt180) cc_final: 0.8666 (ttp-170) REVERT: G 369 ASN cc_start: 0.8660 (p0) cc_final: 0.8391 (p0) REVERT: G 386 MET cc_start: 0.8872 (mmp) cc_final: 0.8580 (mmm) REVERT: G 400 TYR cc_start: 0.7122 (m-80) cc_final: 0.5223 (m-80) REVERT: G 475 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8495 (t) REVERT: G 478 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7361 (pp30) REVERT: G 484 TYR cc_start: 0.9088 (m-80) cc_final: 0.8687 (m-10) REVERT: G 510 GLU cc_start: 0.8219 (mp0) cc_final: 0.7893 (mp0) REVERT: H 32 TYR cc_start: 0.8675 (m-10) cc_final: 0.8350 (m-10) REVERT: H 33 ASN cc_start: 0.8216 (t0) cc_final: 0.7637 (t0) REVERT: H 75 GLU cc_start: 0.8357 (mp0) cc_final: 0.8083 (mp0) REVERT: H 82 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8885 (mtm) REVERT: H 93 HIS cc_start: 0.8909 (p-80) cc_final: 0.8628 (p90) REVERT: H 131 PHE cc_start: 0.9130 (m-80) cc_final: 0.8582 (m-80) REVERT: H 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8256 (tmtt) REVERT: H 230 ASN cc_start: 0.8208 (t0) cc_final: 0.7269 (t0) REVERT: H 231 ARG cc_start: 0.8563 (mmp80) cc_final: 0.8270 (mmp-170) REVERT: H 274 ASP cc_start: 0.9038 (t70) cc_final: 0.8701 (t70) REVERT: H 286 MET cc_start: 0.8467 (mtp) cc_final: 0.8180 (mtp) REVERT: H 309 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8000 (pt0) REVERT: H 343 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 400 TYR cc_start: 0.7561 (m-10) cc_final: 0.7322 (m-10) REVERT: H 493 ARG cc_start: 0.9028 (ttp-170) cc_final: 0.8660 (ttp-170) REVERT: H 510 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8065 (tm-30) outliers start: 193 outliers final: 111 residues processed: 1133 average time/residue: 0.1893 time to fit residues: 350.1408 Evaluate side-chains 1051 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 925 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain J residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 38 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 311 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 129 optimal weight: 0.0870 chunk 184 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN B 21 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN C 94 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 465 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 478 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097175 restraints weight = 51737.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101135 restraints weight = 27005.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.103844 restraints weight = 17205.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.105657 restraints weight = 12483.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107000 restraints weight = 9974.824| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32073 Z= 0.144 Angle : 0.764 15.369 43488 Z= 0.377 Chirality : 0.048 0.388 4968 Planarity : 0.004 0.068 5448 Dihedral : 13.411 89.240 5392 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 7.12 % Allowed : 24.60 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.63 (0.12), residues: 3968 helix: -1.37 (0.14), residues: 1272 sheet: -2.04 (0.24), residues: 382 loop : -1.94 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 407 TYR 0.034 0.002 TYR F 484 PHE 0.021 0.001 PHE D 165 HIS 0.011 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00328 (32072) covalent geometry : angle 0.76376 (43488) hydrogen bonds : bond 0.03741 ( 961) hydrogen bonds : angle 5.79834 ( 2700) Misc. bond : bond 0.00238 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 978 time to evaluate : 1.239 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: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8189 (ttm-80) REVERT: A 110 TYR cc_start: 0.8272 (t80) cc_final: 0.7605 (t80) REVERT: A 230 ASN cc_start: 0.9134 (t0) cc_final: 0.8926 (t0) REVERT: A 238 LYS cc_start: 0.8344 (mtmp) cc_final: 0.8072 (mtmm) REVERT: A 279 ASN cc_start: 0.8623 (t0) cc_final: 0.7598 (t0) REVERT: A 319 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7165 (t0) REVERT: A 352 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 353 TYR cc_start: 0.9034 (t80) cc_final: 0.8741 (t80) REVERT: A 404 ASP cc_start: 0.8488 (t70) cc_final: 0.8202 (t0) REVERT: A 409 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8680 (ttmm) REVERT: A 412 ARG cc_start: 0.7325 (ttp80) cc_final: 0.7020 (ptt90) REVERT: A 466 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.7941 (t-90) REVERT: A 478 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: A 489 LYS cc_start: 0.9314 (mttt) cc_final: 0.8879 (mmtp) REVERT: A 500 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8812 (tm-30) REVERT: B 103 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: B 160 SER cc_start: 0.8523 (t) cc_final: 0.7774 (m) REVERT: B 231 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8659 (mmp80) REVERT: B 259 ARG cc_start: 0.8702 (mtp-110) cc_final: 0.8125 (ttm-80) REVERT: B 312 ASN cc_start: 0.9451 (m-40) cc_final: 0.8646 (t0) REVERT: B 334 GLN cc_start: 0.8912 (mt0) cc_final: 0.8430 (mt0) REVERT: B 335 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 408 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 409 LYS cc_start: 0.8224 (mttp) cc_final: 0.7769 (mmtt) REVERT: B 412 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7266 (ptt90) REVERT: B 448 GLN cc_start: 0.8529 (tt0) cc_final: 0.8301 (pm20) REVERT: B 482 MET cc_start: 0.8698 (mtp) cc_final: 0.8036 (ttm) REVERT: B 487 GLU cc_start: 0.9087 (tt0) cc_final: 0.8348 (tt0) REVERT: C 25 ASN cc_start: 0.8512 (t0) cc_final: 0.8114 (t0) REVERT: C 36 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8838 (pp) REVERT: C 75 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 105 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8191 (ttp80) REVERT: C 134 LYS cc_start: 0.9325 (ptmm) cc_final: 0.9018 (tptt) REVERT: C 150 MET cc_start: 0.8038 (tpp) cc_final: 0.7764 (tpp) REVERT: C 164 ASP cc_start: 0.6875 (m-30) cc_final: 0.6104 (m-30) REVERT: C 179 MET cc_start: 0.7473 (pp-130) cc_final: 0.7263 (pp-130) REVERT: C 182 ARG cc_start: 0.8083 (tpm170) cc_final: 0.7552 (tpp-160) REVERT: C 206 LYS cc_start: 0.9147 (tppp) cc_final: 0.8774 (mmmm) REVERT: C 218 LEU cc_start: 0.9484 (pt) cc_final: 0.8984 (tt) REVERT: C 224 ARG cc_start: 0.8909 (ttt-90) cc_final: 0.8414 (ttm-80) REVERT: C 238 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8419 (mmmt) REVERT: C 279 ASN cc_start: 0.8909 (t0) cc_final: 0.8287 (t0) REVERT: C 369 ASN cc_start: 0.8634 (p0) cc_final: 0.7949 (p0) REVERT: C 386 MET cc_start: 0.8500 (mpm) cc_final: 0.8004 (mpm) REVERT: C 450 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (ptpp) REVERT: C 468 CYS cc_start: 0.8801 (t) cc_final: 0.8337 (t) REVERT: C 478 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: C 483 MET cc_start: 0.9235 (tmm) cc_final: 0.8684 (tmm) REVERT: C 484 TYR cc_start: 0.9054 (m-80) cc_final: 0.8567 (m-10) REVERT: D 32 TYR cc_start: 0.8693 (m-10) cc_final: 0.8373 (m-10) REVERT: D 103 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: D 111 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7350 (mm-30) REVERT: D 199 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8929 (tm-30) REVERT: D 227 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9117 (mm) REVERT: D 231 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7786 (mmm160) REVERT: D 235 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (pp) REVERT: D 277 GLN cc_start: 0.8993 (tp40) cc_final: 0.8516 (tp40) REVERT: D 285 ASN cc_start: 0.9223 (m110) cc_final: 0.8903 (m110) REVERT: D 319 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.6954 (t0) REVERT: D 327 SER cc_start: 0.9040 (p) cc_final: 0.8754 (t) REVERT: D 343 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 359 VAL cc_start: 0.9295 (t) cc_final: 0.9068 (p) REVERT: D 482 MET cc_start: 0.9237 (mtp) cc_final: 0.8930 (mtp) REVERT: D 483 MET cc_start: 0.9813 (tmm) cc_final: 0.9412 (tmm) REVERT: E 72 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9143 (t) REVERT: E 75 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7856 (mp0) REVERT: E 110 TYR cc_start: 0.8055 (t80) cc_final: 0.7565 (t80) REVERT: E 150 MET cc_start: 0.7006 (tmt) cc_final: 0.6374 (tmt) REVERT: E 238 LYS cc_start: 0.8296 (mtmm) cc_final: 0.8032 (mtmm) REVERT: E 241 LYS cc_start: 0.9201 (mptt) cc_final: 0.8792 (ttmm) REVERT: E 279 ASN cc_start: 0.8524 (t0) cc_final: 0.7615 (t0) REVERT: E 335 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 364 ASP cc_start: 0.9094 (t0) cc_final: 0.8747 (t0) REVERT: E 466 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8137 (t-90) REVERT: F 16 ASP cc_start: 0.8782 (t0) cc_final: 0.8369 (t0) REVERT: F 105 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8553 (mtt-85) REVERT: F 110 TYR cc_start: 0.8703 (t80) cc_final: 0.8461 (t80) REVERT: F 114 PHE cc_start: 0.9036 (m-10) cc_final: 0.8747 (m-80) REVERT: F 203 ARG cc_start: 0.9082 (mtm110) cc_final: 0.8762 (mtm110) REVERT: F 206 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8604 (mtpt) REVERT: F 259 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8208 (ttm-80) REVERT: F 319 ASP cc_start: 0.8098 (t0) cc_final: 0.7828 (m-30) REVERT: F 395 GLU cc_start: 0.8746 (mp0) cc_final: 0.8525 (mp0) REVERT: F 409 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8037 (mttt) REVERT: F 412 ARG cc_start: 0.8135 (ttp80) cc_final: 0.6854 (ptt90) REVERT: F 482 MET cc_start: 0.8599 (mtp) cc_final: 0.7801 (ttm) REVERT: F 487 GLU cc_start: 0.9158 (tt0) cc_final: 0.8377 (tt0) REVERT: G 75 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8021 (mm-30) REVERT: G 78 MET cc_start: 0.8487 (tpp) cc_final: 0.8168 (tpp) REVERT: G 105 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8527 (ttp80) REVERT: G 106 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8540 (ttpt) REVERT: G 195 LYS cc_start: 0.9254 (pmmt) cc_final: 0.8690 (mttt) REVERT: G 277 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7816 (tm-30) REVERT: G 279 ASN cc_start: 0.8579 (t0) cc_final: 0.8379 (t0) REVERT: G 369 ASN cc_start: 0.8689 (p0) cc_final: 0.8292 (p0) REVERT: G 386 MET cc_start: 0.9068 (mmp) cc_final: 0.8774 (mmm) REVERT: G 390 LEU cc_start: 0.8979 (mp) cc_final: 0.8753 (mp) REVERT: G 478 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: G 510 GLU cc_start: 0.8150 (mp0) cc_final: 0.7825 (mp0) REVERT: H 32 TYR cc_start: 0.8651 (m-10) cc_final: 0.8418 (m-10) REVERT: H 33 ASN cc_start: 0.8321 (t0) cc_final: 0.7768 (t0) REVERT: H 65 LEU cc_start: 0.9060 (mt) cc_final: 0.8813 (mt) REVERT: H 75 GLU cc_start: 0.8244 (mp0) cc_final: 0.7929 (mt-10) REVERT: H 82 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8957 (mtm) REVERT: H 93 HIS cc_start: 0.8976 (p-80) cc_final: 0.8623 (p90) REVERT: H 99 PHE cc_start: 0.9246 (t80) cc_final: 0.8904 (t80) REVERT: H 131 PHE cc_start: 0.9083 (m-80) cc_final: 0.8799 (m-80) REVERT: H 228 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8276 (tmtt) REVERT: H 230 ASN cc_start: 0.8208 (t0) cc_final: 0.7293 (t0) REVERT: H 231 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8252 (mmp-170) REVERT: H 274 ASP cc_start: 0.9055 (t70) cc_final: 0.8435 (t70) REVERT: H 319 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6738 (t70) REVERT: H 343 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7566 (tm-30) REVERT: H 359 VAL cc_start: 0.9272 (t) cc_final: 0.8868 (p) REVERT: H 483 MET cc_start: 0.9614 (tmm) cc_final: 0.9393 (tmm) REVERT: H 493 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8735 (ttp-170) outliers start: 233 outliers final: 145 residues processed: 1098 average time/residue: 0.1879 time to fit residues: 339.6713 Evaluate side-chains 1081 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 918 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 0.6980 chunk 274 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS E 283 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS H 334 GLN ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.094415 restraints weight = 52388.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098193 restraints weight = 27765.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.100760 restraints weight = 17910.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.102552 restraints weight = 13169.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103839 restraints weight = 10580.930| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32073 Z= 0.187 Angle : 0.779 15.225 43488 Z= 0.385 Chirality : 0.049 0.421 4968 Planarity : 0.004 0.058 5448 Dihedral : 12.980 87.607 5386 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.04 % Rotamer: Outliers : 7.70 % Allowed : 25.92 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.38 (0.13), residues: 3968 helix: -1.10 (0.14), residues: 1268 sheet: -1.81 (0.25), residues: 390 loop : -1.85 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 203 TYR 0.038 0.002 TYR F 484 PHE 0.020 0.001 PHE D 165 HIS 0.011 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00430 (32072) covalent geometry : angle 0.77932 (43488) hydrogen bonds : bond 0.03756 ( 961) hydrogen bonds : angle 5.74958 ( 2700) Misc. bond : bond 0.00262 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 942 time to evaluate : 1.132 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: symmetry clash REVERT: A 34 ASP cc_start: 0.8718 (t0) cc_final: 0.8210 (t70) REVERT: A 103 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8784 (tp30) REVERT: A 105 ARG cc_start: 0.8784 (mtp-110) cc_final: 0.8227 (ttm-80) REVERT: A 230 ASN cc_start: 0.9181 (t0) cc_final: 0.8895 (t0) REVERT: A 238 LYS cc_start: 0.8446 (mtmp) cc_final: 0.8138 (mtmm) REVERT: A 279 ASN cc_start: 0.8624 (t0) cc_final: 0.7722 (t0) REVERT: A 319 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7101 (t0) REVERT: A 352 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 353 TYR cc_start: 0.9069 (t80) cc_final: 0.8827 (t80) REVERT: A 404 ASP cc_start: 0.8532 (t70) cc_final: 0.8115 (t0) REVERT: A 409 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8711 (ttmm) REVERT: A 412 ARG cc_start: 0.7537 (ttp80) cc_final: 0.6999 (ptt90) REVERT: A 466 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.7942 (t-90) REVERT: A 478 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: A 489 LYS cc_start: 0.9344 (mttt) cc_final: 0.9132 (mmtp) REVERT: A 500 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8769 (tm-30) REVERT: B 22 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: B 103 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: B 160 SER cc_start: 0.8476 (t) cc_final: 0.7823 (m) REVERT: B 231 ARG cc_start: 0.8871 (mmt-90) cc_final: 0.8615 (mmp80) REVERT: B 259 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8273 (ttm-80) REVERT: B 334 GLN cc_start: 0.8929 (mt0) cc_final: 0.8485 (mt0) REVERT: B 335 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 352 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7884 (pp20) REVERT: B 408 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 409 LYS cc_start: 0.8235 (mttp) cc_final: 0.7773 (mmtp) REVERT: B 412 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7193 (ptt90) REVERT: B 482 MET cc_start: 0.8676 (mtp) cc_final: 0.8094 (ttm) REVERT: B 487 GLU cc_start: 0.9069 (tt0) cc_final: 0.8336 (tt0) REVERT: C 25 ASN cc_start: 0.8569 (t0) cc_final: 0.8072 (t0) REVERT: C 36 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 75 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: C 105 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8234 (ttp80) REVERT: C 110 TYR cc_start: 0.8147 (t80) cc_final: 0.7938 (t80) REVERT: C 149 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8412 (tmm-80) REVERT: C 150 MET cc_start: 0.8023 (tpp) cc_final: 0.7724 (tpp) REVERT: C 164 ASP cc_start: 0.6947 (m-30) cc_final: 0.6312 (m-30) REVERT: C 179 MET cc_start: 0.7547 (pp-130) cc_final: 0.7289 (pp-130) REVERT: C 182 ARG cc_start: 0.8151 (tpm170) cc_final: 0.7625 (tpp-160) REVERT: C 192 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 206 LYS cc_start: 0.9130 (tppp) cc_final: 0.8678 (mmmm) REVERT: C 218 LEU cc_start: 0.9488 (pt) cc_final: 0.9008 (tt) REVERT: C 224 ARG cc_start: 0.8970 (ttt-90) cc_final: 0.8425 (ttm-80) REVERT: C 279 ASN cc_start: 0.8939 (t0) cc_final: 0.8324 (t0) REVERT: C 297 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9064 (tm) REVERT: C 309 GLN cc_start: 0.8722 (pt0) cc_final: 0.8505 (pt0) REVERT: C 369 ASN cc_start: 0.8640 (p0) cc_final: 0.8082 (p0) REVERT: C 386 MET cc_start: 0.8451 (mpm) cc_final: 0.7932 (mpm) REVERT: C 468 CYS cc_start: 0.8843 (t) cc_final: 0.8382 (t) REVERT: C 478 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: C 483 MET cc_start: 0.9255 (tmm) cc_final: 0.8736 (tmm) REVERT: C 484 TYR cc_start: 0.9136 (m-80) cc_final: 0.8691 (m-10) REVERT: C 510 GLU cc_start: 0.8331 (mp0) cc_final: 0.8102 (mp0) REVERT: D 32 TYR cc_start: 0.8742 (m-10) cc_final: 0.8348 (m-10) REVERT: D 103 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: D 111 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 199 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8903 (tm-30) REVERT: D 235 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7779 (pp) REVERT: D 277 GLN cc_start: 0.9155 (tp40) cc_final: 0.8657 (tp40) REVERT: D 285 ASN cc_start: 0.9228 (m110) cc_final: 0.8912 (m110) REVERT: D 319 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6905 (t0) REVERT: D 327 SER cc_start: 0.9071 (p) cc_final: 0.8753 (t) REVERT: D 343 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8327 (tm-30) REVERT: D 359 VAL cc_start: 0.9338 (t) cc_final: 0.9116 (p) REVERT: D 482 MET cc_start: 0.9271 (mtp) cc_final: 0.8933 (mtp) REVERT: D 483 MET cc_start: 0.9816 (tmm) cc_final: 0.9544 (tmm) REVERT: E 72 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9101 (t) REVERT: E 75 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7686 (mp0) REVERT: E 92 HIS cc_start: 0.8481 (p-80) cc_final: 0.8195 (p90) REVERT: E 150 MET cc_start: 0.7022 (tmt) cc_final: 0.6376 (tmt) REVERT: E 238 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8069 (mtmm) REVERT: E 241 LYS cc_start: 0.9181 (mptt) cc_final: 0.8800 (ttmm) REVERT: E 279 ASN cc_start: 0.8498 (t0) cc_final: 0.7592 (t0) REVERT: E 286 MET cc_start: 0.8615 (tmm) cc_final: 0.8398 (tmm) REVERT: E 364 ASP cc_start: 0.9019 (t0) cc_final: 0.8760 (t0) REVERT: E 382 SER cc_start: 0.9622 (m) cc_final: 0.9389 (t) REVERT: E 466 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8169 (t-90) REVERT: F 16 ASP cc_start: 0.8763 (t0) cc_final: 0.8425 (t0) REVERT: F 103 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: F 105 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8587 (mtt-85) REVERT: F 110 TYR cc_start: 0.8741 (t80) cc_final: 0.8526 (t80) REVERT: F 114 PHE cc_start: 0.9076 (m-10) cc_final: 0.8766 (m-80) REVERT: F 199 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: F 203 ARG cc_start: 0.9081 (mtm110) cc_final: 0.8779 (mtm110) REVERT: F 319 ASP cc_start: 0.8139 (t0) cc_final: 0.7774 (t0) REVERT: F 352 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: F 412 ARG cc_start: 0.8216 (ttp80) cc_final: 0.6859 (ptt90) REVERT: F 482 MET cc_start: 0.8660 (mtp) cc_final: 0.7977 (ttm) REVERT: F 487 GLU cc_start: 0.9147 (tt0) cc_final: 0.8388 (tt0) REVERT: G 75 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7924 (mm-30) REVERT: G 103 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8131 (mm-30) REVERT: G 105 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8502 (ttp80) REVERT: G 106 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8546 (ttpt) REVERT: G 132 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8101 (mm-30) REVERT: G 195 LYS cc_start: 0.9331 (pmmt) cc_final: 0.8613 (tttt) REVERT: G 386 MET cc_start: 0.9069 (mmp) cc_final: 0.8841 (mmm) REVERT: G 510 GLU cc_start: 0.8181 (mp0) cc_final: 0.7860 (mp0) REVERT: H 33 ASN cc_start: 0.8468 (t0) cc_final: 0.7948 (t0) REVERT: H 65 LEU cc_start: 0.9191 (mt) cc_final: 0.8953 (mm) REVERT: H 75 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: H 82 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (mtm) REVERT: H 93 HIS cc_start: 0.9002 (p-80) cc_final: 0.8645 (p90) REVERT: H 103 GLU cc_start: 0.8488 (mp0) cc_final: 0.8141 (mp0) REVERT: H 131 PHE cc_start: 0.9152 (m-80) cc_final: 0.8641 (m-80) REVERT: H 228 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8356 (tmtt) REVERT: H 230 ASN cc_start: 0.8082 (t0) cc_final: 0.7196 (t0) REVERT: H 231 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8256 (mmp-170) REVERT: H 274 ASP cc_start: 0.9112 (t70) cc_final: 0.8743 (t70) REVERT: H 343 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7670 (tm-30) REVERT: H 359 VAL cc_start: 0.9327 (t) cc_final: 0.8990 (p) REVERT: H 395 GLU cc_start: 0.8759 (mp0) cc_final: 0.8469 (pm20) REVERT: H 399 GLU cc_start: 0.8224 (pm20) cc_final: 0.7980 (pm20) REVERT: H 478 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8772 (pt0) REVERT: H 493 ARG cc_start: 0.9038 (ttp-170) cc_final: 0.8793 (ttp-170) REVERT: K 1 MET cc_start: 0.5832 (pmm) cc_final: 0.5103 (pmm) outliers start: 252 outliers final: 167 residues processed: 1077 average time/residue: 0.1880 time to fit residues: 336.1163 Evaluate side-chains 1092 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 901 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain H residue 478 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8957 > 50: distance: 34 - 40: 14.924 distance: 40 - 41: 26.012 distance: 41 - 42: 30.544 distance: 41 - 44: 18.024 distance: 42 - 43: 36.781 distance: 42 - 47: 45.929 distance: 44 - 45: 38.686 distance: 44 - 46: 17.448 distance: 47 - 48: 24.386 distance: 48 - 49: 58.922 distance: 48 - 51: 29.535 distance: 49 - 50: 56.335 distance: 49 - 56: 38.954 distance: 51 - 52: 15.885 distance: 52 - 53: 10.919 distance: 53 - 54: 8.451 distance: 54 - 55: 11.033 distance: 56 - 57: 16.897 distance: 57 - 58: 25.530 distance: 57 - 60: 25.378 distance: 58 - 59: 34.528 distance: 58 - 67: 15.429 distance: 60 - 61: 19.334 distance: 61 - 62: 8.325 distance: 62 - 63: 12.199 distance: 63 - 64: 10.168 distance: 64 - 65: 4.327 distance: 64 - 66: 7.440 distance: 67 - 68: 26.510 distance: 68 - 69: 31.201 distance: 68 - 71: 13.051 distance: 69 - 70: 28.541 distance: 69 - 76: 50.999 distance: 71 - 72: 13.690 distance: 72 - 73: 16.781 distance: 73 - 74: 14.350 distance: 73 - 75: 17.208 distance: 76 - 77: 45.099 distance: 77 - 78: 15.878 distance: 77 - 80: 40.781 distance: 78 - 79: 17.200 distance: 78 - 84: 15.113 distance: 80 - 81: 25.532 distance: 81 - 82: 21.703 distance: 81 - 83: 13.180 distance: 84 - 85: 42.866 distance: 85 - 86: 17.558 distance: 85 - 88: 38.414 distance: 86 - 87: 26.735 distance: 86 - 92: 17.159 distance: 88 - 89: 45.562 distance: 89 - 90: 9.879 distance: 89 - 91: 25.199 distance: 92 - 93: 33.057 distance: 93 - 94: 57.056 distance: 93 - 96: 27.953 distance: 94 - 95: 53.421 distance: 94 - 99: 44.295 distance: 96 - 97: 20.890 distance: 96 - 98: 9.313 distance: 99 - 100: 23.428 distance: 100 - 101: 67.894 distance: 100 - 103: 46.827 distance: 101 - 102: 68.896 distance: 101 - 106: 23.353 distance: 103 - 104: 40.764 distance: 103 - 105: 17.642 distance: 106 - 107: 53.701 distance: 107 - 108: 25.239 distance: 107 - 110: 40.378 distance: 108 - 109: 53.066 distance: 108 - 111: 44.785 distance: 111 - 112: 31.946 distance: 111 - 117: 57.229 distance: 112 - 113: 50.006 distance: 112 - 115: 57.246 distance: 113 - 114: 51.939 distance: 113 - 118: 22.746 distance: 115 - 116: 16.224 distance: 116 - 117: 30.117